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1 <tool id="plink2" name="PLINK 2" version="2.00a2.3">
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2 <requirements>
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3 <requirement type="package" version="2.00a2.3">plink</requirement>
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4 </requirements>
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5 <code file="plink_code_file.py" />
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <version_command>plink2 --version</version_command>
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10 <command><![CDATA[
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11 plink2
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12
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13 #if str($CONDITIONAL_pfile.CONDITIONAL_SELECT_pfile) == "set":
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14 --pfile
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15
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16
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17 #if $str($CONDITIONAL_pfile.pfile_MOD_0_0):
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18 '${CONDITIONAL_pfile.pfile_MOD_0_0}'
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19 #end if
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20
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21 #if $str($CONDITIONAL_pfile.pfile_MOD_1_0):
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22 '${CONDITIONAL_pfile.pfile_MOD_1_0}'
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23 #end if
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24
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25 #end if
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26
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27 #if str($CONDITIONAL_pgen.CONDITIONAL_SELECT_pgen) == "set":
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28 --pgen
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29
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30
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31 #if $CONDITIONAL_pgen.pgen_MOD_0_0:
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32 '${CONDITIONAL_pgen.pgen_MOD_0_0}'
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33 #end if
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34
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35 #end if
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36
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37 #if str($CONDITIONAL_pvar.CONDITIONAL_SELECT_pvar) == "set":
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38 --pvar
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39
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40
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41 #if $CONDITIONAL_pvar.pvar_MOD_0_0:
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42 '${CONDITIONAL_pvar.pvar_MOD_0_0}'
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43 #end if
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44
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45 #end if
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46
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47 #if str($CONDITIONAL_psam.CONDITIONAL_SELECT_psam) == "set":
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48 --psam
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49
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50
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51 #if $CONDITIONAL_psam.psam_MOD_0_0:
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52 '${CONDITIONAL_psam.psam_MOD_0_0}'
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53 #end if
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54
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55 #end if
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56
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57 #if str($CONDITIONAL_bpfile.CONDITIONAL_SELECT_bpfile) == "set":
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58 --bpfile
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59
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60
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61 #if $str($CONDITIONAL_bpfile.bpfile_MOD_0_0):
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62 '${CONDITIONAL_bpfile.bpfile_MOD_0_0}'
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63 #end if
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64
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65 #if $str($CONDITIONAL_bpfile.bpfile_MOD_1_0):
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66 '${CONDITIONAL_bpfile.bpfile_MOD_1_0}'
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67 #end if
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68
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69 #end if
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70
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71 #if str($CONDITIONAL_keep_autoconv.CONDITIONAL_SELECT_keep_autoconv) == "set":
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72 --keep-autoconv
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73
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74
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75 #end if
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76
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77 #if str($CONDITIONAL_no_fid.CONDITIONAL_SELECT_no_fid) == "set":
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78 --no-fid
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79
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80
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81 #end if
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82
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83 #if str($CONDITIONAL_no_parents.CONDITIONAL_SELECT_no_parents) == "set":
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84 --no-parents
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85
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86
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87 #end if
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88
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89 #if str($CONDITIONAL_no_sex.CONDITIONAL_SELECT_no_sex) == "set":
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90 --no-sex
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91
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92
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93 #end if
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94
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95 #if str($CONDITIONAL_vcf.CONDITIONAL_SELECT_vcf) == "set":
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96 --vcf
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97
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98
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99 #if $CONDITIONAL_vcf.vcf_MOD_0_0:
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100 '${CONDITIONAL_vcf.vcf_MOD_0_0}'
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101 #end if
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102
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103 #if $str($CONDITIONAL_vcf.vcf_MOD_1_0):
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104 '${CONDITIONAL_vcf.vcf_MOD_1_0}'
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105 #end if
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106
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107 #end if
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108
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109 #if str($CONDITIONAL_bcf.CONDITIONAL_SELECT_bcf) == "set":
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110 --bcf
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111
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112
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113 #if $CONDITIONAL_bcf.bcf_MOD_0_0:
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114 '${CONDITIONAL_bcf.bcf_MOD_0_0}'
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115 #end if
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116
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117 #if $str($CONDITIONAL_bcf.bcf_MOD_1_0):
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118 '${CONDITIONAL_bcf.bcf_MOD_1_0}'
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119 #end if
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120
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121 #end if
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122
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123 #if str($CONDITIONAL_bgen.CONDITIONAL_SELECT_bgen) == "set":
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124 --bgen
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125
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126
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127 #if $CONDITIONAL_bgen.bgen_MOD_0_0:
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128 '${CONDITIONAL_bgen.bgen_MOD_0_0}'
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129 #end if
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130
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131 #if $str($CONDITIONAL_bgen.bgen_MOD_1_0):
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132 '${CONDITIONAL_bgen.bgen_MOD_1_0}'
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133 #end if
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134
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135 #if $str($CONDITIONAL_bgen.bgen_MOD_2_0):
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136 '${CONDITIONAL_bgen.bgen_MOD_2_0}'
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137 #end if
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138
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139 #end if
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140
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141 #if str($CONDITIONAL_gen.CONDITIONAL_SELECT_gen) == "set":
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142 --gen
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143
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144
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145 #if $CONDITIONAL_gen.gen_MOD_0_0:
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146 '${CONDITIONAL_gen.gen_MOD_0_0}'
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147 #end if
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148
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149 #if $str($CONDITIONAL_gen.gen_MOD_1_0):
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150 '${CONDITIONAL_gen.gen_MOD_1_0}'
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151 #end if
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152
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153 #end if
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154
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155 #if str($CONDITIONAL_sample.CONDITIONAL_SELECT_sample) == "set":
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156 --sample
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157
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158
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159 #if $CONDITIONAL_sample.sample_MOD_0_0:
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160 '${CONDITIONAL_sample.sample_MOD_0_0}'
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161 #end if
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162
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163 #end if
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164
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165 #if str($CONDITIONAL_haps.CONDITIONAL_SELECT_haps) == "set":
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166 --haps
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167
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168
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169 #if $CONDITIONAL_haps.haps_MOD_0_0:
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170 '${CONDITIONAL_haps.haps_MOD_0_0}'
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171 #end if
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172
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173 #if $str($CONDITIONAL_haps.CONDITIONAL_haps_MOD_1.CONDITIONAL_SELECT_haps_MOD_1) == 'from_list'
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174 '${CONDITIONAL_haps.CONDITIONAL_haps_MOD_1.haps_MOD_1}'
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175 #end if
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176
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177
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178 #end if
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179
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180 #if str($CONDITIONAL_legend.CONDITIONAL_SELECT_legend) == "set":
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181 --legend
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182
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183
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184 #if $CONDITIONAL_legend.legend_MOD_0_0:
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185 '${CONDITIONAL_legend.legend_MOD_0_0}'
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186 #end if
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187
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188 #if $str($CONDITIONAL_legend.legend_MOD_1_0):
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189 '${CONDITIONAL_legend.legend_MOD_1_0}'
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190 #end if
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191
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192 #end if
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193
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194 #if str($CONDITIONAL_map.CONDITIONAL_SELECT_map) == "set":
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195 --map
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196
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197
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198 #if $CONDITIONAL_map.map_MOD_0_0:
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199 '${CONDITIONAL_map.map_MOD_0_0}'
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200 #end if
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201
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202 #end if
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203
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204 #if str($CONDITIONAL_import_dosage.CONDITIONAL_SELECT_import_dosage) == "set":
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205 --import-dosage
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206
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207
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208 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_0_0):
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209 '${CONDITIONAL_import_dosage.import_dosage_MOD_0_0}'
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210 #end if
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211
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212 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_1_0):
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213 '${CONDITIONAL_import_dosage.import_dosage_MOD_1_0}'
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214 #end if
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215
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216 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_2_0):
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217 '${CONDITIONAL_import_dosage.import_dosage_MOD_2_0}'
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218 #end if
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219
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220 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_3_0):
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221 '${CONDITIONAL_import_dosage.import_dosage_MOD_3_0}'
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222 #end if
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223
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224 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_4_0):
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225 '${CONDITIONAL_import_dosage.import_dosage_MOD_4_0}'
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226 #end if
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227
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228 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_5_0):
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229 '${CONDITIONAL_import_dosage.import_dosage_MOD_5_0}'
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230 #end if
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231
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232 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_6_0):
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233 '${CONDITIONAL_import_dosage.import_dosage_MOD_6_0}'
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234 #end if
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235
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236 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_7_0):
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237 '${CONDITIONAL_import_dosage.import_dosage_MOD_7_0}'
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238 #end if
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239
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240 #if $str($CONDITIONAL_import_dosage.CONDITIONAL_import_dosage_MOD_8.CONDITIONAL_SELECT_import_dosage_MOD_8) == 'from_list'
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241 '${CONDITIONAL_import_dosage.CONDITIONAL_import_dosage_MOD_8.import_dosage_MOD_8}'
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242 #end if
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243
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244
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245 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_9_0):
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246 '${CONDITIONAL_import_dosage.import_dosage_MOD_9_0}'
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247 #end if
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248
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249 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_10_0):
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250 '${CONDITIONAL_import_dosage.import_dosage_MOD_10_0}'
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251 #end if
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252
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253 #if $str($CONDITIONAL_import_dosage.import_dosage_MOD_11_0):
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254 '${CONDITIONAL_import_dosage.import_dosage_MOD_11_0}'
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255 #end if
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256
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257 #end if
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258
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259 #if str($CONDITIONAL_dummy.CONDITIONAL_SELECT_dummy) == "set":
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260 --dummy
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261
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262
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263 #if $str($CONDITIONAL_dummy.dummy_MOD_0_0):
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264 '${CONDITIONAL_dummy.dummy_MOD_0_0}'
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265 #end if
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266
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267 #if $str($CONDITIONAL_dummy.dummy_MOD_1_0):
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268 '${CONDITIONAL_dummy.dummy_MOD_1_0}'
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269 #end if
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270
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271 #if $str($CONDITIONAL_dummy.dummy_MOD_2_0):
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272 '${CONDITIONAL_dummy.dummy_MOD_2_0}'
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273 #end if
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274
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275 #if $str($CONDITIONAL_dummy.dummy_MOD_3_0):
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276 '${CONDITIONAL_dummy.dummy_MOD_3_0}'
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277 #end if
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278
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279 #if $str($CONDITIONAL_dummy.CONDITIONAL_dummy_MOD_4.CONDITIONAL_SELECT_dummy_MOD_4) == 'from_list'
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280 '${CONDITIONAL_dummy.CONDITIONAL_dummy_MOD_4.dummy_MOD_4}'
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281 #end if
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282
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283
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284 #if $str($CONDITIONAL_dummy.dummy_MOD_5_0):
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285 '${CONDITIONAL_dummy.dummy_MOD_5_0}'
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286 #end if
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287
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288 #if $str($CONDITIONAL_dummy.dummy_MOD_6_0):
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289 '${CONDITIONAL_dummy.dummy_MOD_6_0}'
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290 #end if
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291
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292 #if $str($CONDITIONAL_dummy.dummy_MOD_7_0):
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293 '${CONDITIONAL_dummy.dummy_MOD_7_0}'
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294 #end if
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295
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296 #end if
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297
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298 #if str($CONDITIONAL_fa.CONDITIONAL_SELECT_fa) == "set":
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299 --fa
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300
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301
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302 #if $CONDITIONAL_fa.fa_MOD_0_0:
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303 '${CONDITIONAL_fa.fa_MOD_0_0}'
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304 #end if
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305
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306 #end if
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307
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308 #if str($CONDITIONAL_rm_dup.CONDITIONAL_SELECT_rm_dup) == "set":
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309 --rm-dup
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310
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311
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312 #if $str($CONDITIONAL_rm_dup.rm_dup_MOD_0_0):
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313 '${CONDITIONAL_rm_dup.rm_dup_MOD_0_0}'
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314 #end if
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315
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316 #if $str($CONDITIONAL_rm_dup.rm_dup_MOD_1_0):
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317 '${CONDITIONAL_rm_dup.rm_dup_MOD_1_0}'
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318 #end if
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319
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320 #end if
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321
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322 #if str($CONDITIONAL_make_pgen.CONDITIONAL_SELECT_make_pgen) == "set":
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323 --make-pgen
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324
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325
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326 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_0_0):
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327 '${CONDITIONAL_make_pgen.make_pgen_MOD_0_0}'
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328 #end if
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329
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330 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_1_0):
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331 '${CONDITIONAL_make_pgen.make_pgen_MOD_1_0}'
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332 #end if
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333
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334 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_2_0):
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335 '${CONDITIONAL_make_pgen.make_pgen_MOD_2_0}'
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336 #end if
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337
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338 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_3_0):
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339 '${CONDITIONAL_make_pgen.make_pgen_MOD_3_0}'
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340 #end if
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341
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342 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_4_0):
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343 '${CONDITIONAL_make_pgen.make_pgen_MOD_4_0}'
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344 #end if
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345
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346 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_5_0):
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347 '${CONDITIONAL_make_pgen.make_pgen_MOD_5_0}'
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348 #end if
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349
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350 #if $str($CONDITIONAL_make_pgen.make_pgen_MOD_6_0):
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351 '${CONDITIONAL_make_pgen.make_pgen_MOD_6_0}'
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352 #end if
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353
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354 #end if
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355
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356 #if str($CONDITIONAL_make_bpgen.CONDITIONAL_SELECT_make_bpgen) == "set":
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357 --make-bpgen
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358
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359
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360 #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_0_0):
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361 '${CONDITIONAL_make_bpgen.make_bpgen_MOD_0_0}'
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362 #end if
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363
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364 #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_1_0):
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365 '${CONDITIONAL_make_bpgen.make_bpgen_MOD_1_0}'
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366 #end if
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367
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368 #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_2_0):
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369 '${CONDITIONAL_make_bpgen.make_bpgen_MOD_2_0}'
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370 #end if
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371
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372 #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_3_0):
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373 '${CONDITIONAL_make_bpgen.make_bpgen_MOD_3_0}'
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374 #end if
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375
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376 #if $str($CONDITIONAL_make_bpgen.make_bpgen_MOD_4_0):
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377 '${CONDITIONAL_make_bpgen.make_bpgen_MOD_4_0}'
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378 #end if
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379
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380 #end if
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381
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382 #if str($CONDITIONAL_make_bed.CONDITIONAL_SELECT_make_bed) == "set":
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383 --make-bed
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384
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385
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386 #if $str($CONDITIONAL_make_bed.make_bed_MOD_0_0):
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387 '${CONDITIONAL_make_bed.make_bed_MOD_0_0}'
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388 #end if
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389
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390 #if $str($CONDITIONAL_make_bed.make_bed_MOD_1_0):
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391 '${CONDITIONAL_make_bed.make_bed_MOD_1_0}'
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|
392 #end if
|
|
|
393
|
|
|
394 #end if
|
|
|
395
|
|
|
396 #if str($CONDITIONAL_make_just_pvar.CONDITIONAL_SELECT_make_just_pvar) == "set":
|
|
|
397 --make-just-pvar
|
|
|
398
|
|
|
399
|
|
|
400 #if $str($CONDITIONAL_make_just_pvar.make_just_pvar_MOD_0_0):
|
|
|
401 '${CONDITIONAL_make_just_pvar.make_just_pvar_MOD_0_0}'
|
|
|
402 #end if
|
|
|
403
|
|
|
404 #if $str($CONDITIONAL_make_just_pvar.make_just_pvar_MOD_1_0):
|
|
|
405 '${CONDITIONAL_make_just_pvar.make_just_pvar_MOD_1_0}'
|
|
|
406 #end if
|
|
|
407
|
|
|
408 #end if
|
|
|
409
|
|
|
410 #if str($CONDITIONAL_make_just_psam.CONDITIONAL_SELECT_make_just_psam) == "set":
|
|
|
411 --make-just-psam
|
|
|
412
|
|
|
413
|
|
|
414 #if $str($CONDITIONAL_make_just_psam.make_just_psam_MOD_0_0):
|
|
|
415 '${CONDITIONAL_make_just_psam.make_just_psam_MOD_0_0}'
|
|
|
416 #end if
|
|
|
417
|
|
|
418 #end if
|
|
|
419
|
|
|
420 #if str($CONDITIONAL_make_just_bim.CONDITIONAL_SELECT_make_just_bim) == "set":
|
|
|
421 --make-just-bim
|
|
|
422
|
|
|
423
|
|
|
424 #if $str($CONDITIONAL_make_just_bim.make_just_bim_MOD_0_0):
|
|
|
425 '${CONDITIONAL_make_just_bim.make_just_bim_MOD_0_0}'
|
|
|
426 #end if
|
|
|
427
|
|
|
428 #end if
|
|
|
429
|
|
|
430 ${make_just_fam}
|
|
|
431
|
|
|
432 #if str($CONDITIONAL_export.CONDITIONAL_SELECT_export) == "set":
|
|
|
433 --export
|
|
|
434
|
|
|
435
|
|
|
436 #if $str($CONDITIONAL_export.export_MOD_0_0):
|
|
|
437 '${CONDITIONAL_export.export_MOD_0_0}'
|
|
|
438 #end if
|
|
|
439
|
|
|
440 #if $str($CONDITIONAL_export.CONDITIONAL_export_MOD_1.CONDITIONAL_SELECT_export_MOD_1) == 'from_list'
|
|
|
441 '${CONDITIONAL_export.CONDITIONAL_export_MOD_1.export_MOD_1}'
|
|
|
442 #end if
|
|
|
443
|
|
|
444
|
|
|
445 #if $str($CONDITIONAL_export.export_MOD_2_0):
|
|
|
446 '${CONDITIONAL_export.export_MOD_2_0}'
|
|
|
447 #end if
|
|
|
448
|
|
|
449 #if $str($CONDITIONAL_export.export_MOD_3_0):
|
|
|
450 '${CONDITIONAL_export.export_MOD_3_0}'
|
|
|
451 #end if
|
|
|
452
|
|
|
453 #if $str($CONDITIONAL_export.export_MOD_4_0):
|
|
|
454 '${CONDITIONAL_export.export_MOD_4_0}'
|
|
|
455 #end if
|
|
|
456
|
|
|
457 #if $str($CONDITIONAL_export.export_MOD_5_0):
|
|
|
458 '${CONDITIONAL_export.export_MOD_5_0}'
|
|
|
459 #end if
|
|
|
460
|
|
|
461 #if $str($CONDITIONAL_export.export_MOD_6_0):
|
|
|
462 '${CONDITIONAL_export.export_MOD_6_0}'
|
|
|
463 #end if
|
|
|
464
|
|
|
465 #if $str($CONDITIONAL_export.export_MOD_7_0):
|
|
|
466 '${CONDITIONAL_export.export_MOD_7_0}'
|
|
|
467 #end if
|
|
|
468
|
|
|
469 #if $str($CONDITIONAL_export.export_MOD_8_0):
|
|
|
470 '${CONDITIONAL_export.export_MOD_8_0}'
|
|
|
471 #end if
|
|
|
472
|
|
|
473 #if $str($CONDITIONAL_export.export_MOD_9_0):
|
|
|
474 '${CONDITIONAL_export.export_MOD_9_0}'
|
|
|
475 #end if
|
|
|
476
|
|
|
477 #if $str($CONDITIONAL_export.export_MOD_10_0):
|
|
|
478 '${CONDITIONAL_export.export_MOD_10_0}'
|
|
|
479 #end if
|
|
|
480
|
|
|
481 #end if
|
|
|
482
|
|
|
483 #if str($CONDITIONAL_freq.CONDITIONAL_SELECT_freq) == "set":
|
|
|
484 --freq
|
|
|
485
|
|
|
486
|
|
|
487 #if $str($CONDITIONAL_freq.freq_MOD_0_0):
|
|
|
488 '${CONDITIONAL_freq.freq_MOD_0_0}'
|
|
|
489 #end if
|
|
|
490
|
|
|
491 #if $str($CONDITIONAL_freq.freq_MOD_1_0):
|
|
|
492 '${CONDITIONAL_freq.freq_MOD_1_0}'
|
|
|
493 #end if
|
|
|
494
|
|
|
495 #if $str($CONDITIONAL_freq.freq_MOD_2_0):
|
|
|
496 '${CONDITIONAL_freq.freq_MOD_2_0}'
|
|
|
497 #end if
|
|
|
498
|
|
|
499 #if $str($CONDITIONAL_freq.freq_MOD_3_0):
|
|
|
500 '${CONDITIONAL_freq.freq_MOD_3_0}'
|
|
|
501 #end if
|
|
|
502
|
|
|
503 #end if
|
|
|
504
|
|
|
505 #if str($CONDITIONAL_geno_counts.CONDITIONAL_SELECT_geno_counts) == "set":
|
|
|
506 --geno-counts
|
|
|
507
|
|
|
508
|
|
|
509 #if $str($CONDITIONAL_geno_counts.geno_counts_MOD_0_0):
|
|
|
510 '${CONDITIONAL_geno_counts.geno_counts_MOD_0_0}'
|
|
|
511 #end if
|
|
|
512
|
|
|
513 #if $str($CONDITIONAL_geno_counts.geno_counts_MOD_1_0):
|
|
|
514 '${CONDITIONAL_geno_counts.geno_counts_MOD_1_0}'
|
|
|
515 #end if
|
|
|
516
|
|
|
517 #end if
|
|
|
518
|
|
|
519 #if str($CONDITIONAL_sample_counts.CONDITIONAL_SELECT_sample_counts) == "set":
|
|
|
520 --sample-counts
|
|
|
521
|
|
|
522
|
|
|
523 #if $str($CONDITIONAL_sample_counts.sample_counts_MOD_0_0):
|
|
|
524 '${CONDITIONAL_sample_counts.sample_counts_MOD_0_0}'
|
|
|
525 #end if
|
|
|
526
|
|
|
527 #if $str($CONDITIONAL_sample_counts.sample_counts_MOD_1_0):
|
|
|
528 '${CONDITIONAL_sample_counts.sample_counts_MOD_1_0}'
|
|
|
529 #end if
|
|
|
530
|
|
|
531 #end if
|
|
|
532
|
|
|
533 #if str($CONDITIONAL_missing.CONDITIONAL_SELECT_missing) == "set":
|
|
|
534 --missing
|
|
|
535
|
|
|
536
|
|
|
537 #if $str($CONDITIONAL_missing.missing_MOD_0_0):
|
|
|
538 '${CONDITIONAL_missing.missing_MOD_0_0}'
|
|
|
539 #end if
|
|
|
540
|
|
|
541 #if $str($CONDITIONAL_missing.CONDITIONAL_missing_MOD_1.CONDITIONAL_SELECT_missing_MOD_1) == 'from_list'
|
|
|
542 '${CONDITIONAL_missing.CONDITIONAL_missing_MOD_1.missing_MOD_1}'
|
|
|
543 #end if
|
|
|
544
|
|
|
545
|
|
|
546 #if $str($CONDITIONAL_missing.missing_MOD_2_0):
|
|
|
547 '${CONDITIONAL_missing.missing_MOD_2_0}'
|
|
|
548 #end if
|
|
|
549
|
|
|
550 #if $str($CONDITIONAL_missing.missing_MOD_3_0):
|
|
|
551 '${CONDITIONAL_missing.missing_MOD_3_0}'
|
|
|
552 #end if
|
|
|
553
|
|
|
554 #end if
|
|
|
555
|
|
|
556 #if str($CONDITIONAL_hardy.CONDITIONAL_SELECT_hardy) == "set":
|
|
|
557 --hardy
|
|
|
558
|
|
|
559
|
|
|
560 #if $str($CONDITIONAL_hardy.hardy_MOD_0_0):
|
|
|
561 '${CONDITIONAL_hardy.hardy_MOD_0_0}'
|
|
|
562 #end if
|
|
|
563
|
|
|
564 #if $str($CONDITIONAL_hardy.hardy_MOD_1_0):
|
|
|
565 '${CONDITIONAL_hardy.hardy_MOD_1_0}'
|
|
|
566 #end if
|
|
|
567
|
|
|
568 #if $str($CONDITIONAL_hardy.hardy_MOD_2_0):
|
|
|
569 '${CONDITIONAL_hardy.hardy_MOD_2_0}'
|
|
|
570 #end if
|
|
|
571
|
|
|
572 #if $str($CONDITIONAL_hardy.hardy_MOD_3_0):
|
|
|
573 '${CONDITIONAL_hardy.hardy_MOD_3_0}'
|
|
|
574 #end if
|
|
|
575
|
|
|
576 #end if
|
|
|
577
|
|
|
578 #if str($CONDITIONAL_indep_pairwise.CONDITIONAL_SELECT_indep_pairwise) == "set":
|
|
|
579 --indep-pairwise
|
|
|
580
|
|
|
581
|
|
|
582 #if $str($CONDITIONAL_indep_pairwise.indep_pairwise_MOD_0_0):
|
|
|
583 '${CONDITIONAL_indep_pairwise.indep_pairwise_MOD_0_0}'
|
|
|
584 #end if
|
|
|
585
|
|
|
586 #if $str($CONDITIONAL_indep_pairwise.indep_pairwise_MOD_1_0):
|
|
|
587 '${CONDITIONAL_indep_pairwise.indep_pairwise_MOD_1_0}'
|
|
|
588 #end if
|
|
|
589
|
|
|
590 #if $str($CONDITIONAL_indep_pairwise.indep_pairwise_MOD_2_0):
|
|
|
591 '${CONDITIONAL_indep_pairwise.indep_pairwise_MOD_2_0}'
|
|
|
592 #end if
|
|
|
593
|
|
|
594 #if $str($CONDITIONAL_indep_pairwise.indep_pairwise_MOD_3_0):
|
|
|
595 '${CONDITIONAL_indep_pairwise.indep_pairwise_MOD_3_0}'
|
|
|
596 #end if
|
|
|
597
|
|
|
598 #end if
|
|
|
599
|
|
|
600 #if str($CONDITIONAL_ld.CONDITIONAL_SELECT_ld) == "set":
|
|
|
601 --ld
|
|
|
602
|
|
|
603
|
|
|
604 #if $str($CONDITIONAL_ld.ld_MOD_0_0):
|
|
|
605 '${CONDITIONAL_ld.ld_MOD_0_0}'
|
|
|
606 #end if
|
|
|
607
|
|
|
608 #if $str($CONDITIONAL_ld.ld_MOD_1_0):
|
|
|
609 '${CONDITIONAL_ld.ld_MOD_1_0}'
|
|
|
610 #end if
|
|
|
611
|
|
|
612 #if $str($CONDITIONAL_ld.ld_MOD_2_0):
|
|
|
613 '${CONDITIONAL_ld.ld_MOD_2_0}'
|
|
|
614 #end if
|
|
|
615
|
|
|
616 #if $str($CONDITIONAL_ld.ld_MOD_3_0):
|
|
|
617 '${CONDITIONAL_ld.ld_MOD_3_0}'
|
|
|
618 #end if
|
|
|
619
|
|
|
620 #end if
|
|
|
621
|
|
|
622 #if str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_OVERLOADED_SELECT_sample_diff) == "form_0":
|
|
|
623 #if str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_SELECT_sample_diff) == "set":
|
|
|
624 --sample-diff
|
|
|
625
|
|
|
626 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_0_0):
|
|
|
627 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_0_0}'
|
|
|
628 #end if
|
|
|
629 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_1.CONDITIONAL_SELECT_sample_diff_MOD_1) == 'from_list'
|
|
|
630 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_1.sample_diff_MOD_1}'
|
|
|
631 #end if
|
|
|
632
|
|
|
633 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_2_0):
|
|
|
634 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_2_0}'
|
|
|
635 #end if
|
|
|
636 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_3.CONDITIONAL_SELECT_sample_diff_MOD_3) == 'from_list'
|
|
|
637 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_3.sample_diff_MOD_3}'
|
|
|
638 #end if
|
|
|
639
|
|
|
640 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_4_0):
|
|
|
641 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_4_0}'
|
|
|
642 #end if
|
|
|
643 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_5_0):
|
|
|
644 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_5_0}'
|
|
|
645 #end if
|
|
|
646 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_6_0):
|
|
|
647 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_6_0}'
|
|
|
648 #end if
|
|
|
649 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_7_0):
|
|
|
650 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_7_0}'
|
|
|
651 #end if
|
|
|
652 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_8.CONDITIONAL_SELECT_sample_diff_MOD_8) == 'from_list'
|
|
|
653 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_8.sample_diff_MOD_8}'
|
|
|
654 #end if
|
|
|
655
|
|
|
656 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_9_0):
|
|
|
657 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_9_0}'
|
|
|
658 #end if
|
|
|
659 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_10_0):
|
|
|
660 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_10_0}'
|
|
|
661 #end if
|
|
|
662 #end if
|
|
|
663 #end if
|
|
|
664
|
|
|
665 #if str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_OVERLOADED_SELECT_sample_diff) == "form_1":
|
|
|
666 #if str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_SELECT_sample_diff) == "set":
|
|
|
667 --sample-diff
|
|
|
668
|
|
|
669 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_0_0):
|
|
|
670 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_0_0}'
|
|
|
671 #end if
|
|
|
672 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_1.CONDITIONAL_SELECT_sample_diff_MOD_1) == 'from_list'
|
|
|
673 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_1.sample_diff_MOD_1}'
|
|
|
674 #end if
|
|
|
675
|
|
|
676 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_2_0):
|
|
|
677 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_2_0}'
|
|
|
678 #end if
|
|
|
679 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_3.CONDITIONAL_SELECT_sample_diff_MOD_3) == 'from_list'
|
|
|
680 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.CONDITIONAL_sample_diff_MOD_3.sample_diff_MOD_3}'
|
|
|
681 #end if
|
|
|
682
|
|
|
683 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_4_0):
|
|
|
684 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_4_0}'
|
|
|
685 #end if
|
|
|
686 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_5_0):
|
|
|
687 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_5_0}'
|
|
|
688 #end if
|
|
|
689 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_6_0):
|
|
|
690 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_6_0}'
|
|
|
691 #end if
|
|
|
692 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_7_0):
|
|
|
693 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_7_0}'
|
|
|
694 #end if
|
|
|
695 #if $str($CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_8_0):
|
|
|
696 '${CONDITIONAL_OVERLOADED_sample_diff.CONDITIONAL_sample_diff.sample_diff_MOD_8_0}'
|
|
|
697 #end if
|
|
|
698 #end if
|
|
|
699 #end if
|
|
|
700
|
|
|
701 #if str($CONDITIONAL_make_king.CONDITIONAL_SELECT_make_king) == "set":
|
|
|
702 --make-king
|
|
|
703
|
|
|
704
|
|
|
705 #if $str($CONDITIONAL_make_king.CONDITIONAL_make_king_MOD_0.CONDITIONAL_SELECT_make_king_MOD_0) == 'from_list'
|
|
|
706 '${CONDITIONAL_make_king.CONDITIONAL_make_king_MOD_0.make_king_MOD_0}'
|
|
|
707 #end if
|
|
|
708
|
|
|
709
|
|
|
710 #if $str($CONDITIONAL_make_king.CONDITIONAL_make_king_MOD_1.CONDITIONAL_SELECT_make_king_MOD_1) == 'from_list'
|
|
|
711 '${CONDITIONAL_make_king.CONDITIONAL_make_king_MOD_1.make_king_MOD_1}'
|
|
|
712 #end if
|
|
|
713
|
|
|
714
|
|
|
715 #end if
|
|
|
716
|
|
|
717 #if str($CONDITIONAL_make_king_table.CONDITIONAL_SELECT_make_king_table) == "set":
|
|
|
718 --make-king-table
|
|
|
719
|
|
|
720
|
|
|
721 #if $str($CONDITIONAL_make_king_table.make_king_table_MOD_0_0):
|
|
|
722 '${CONDITIONAL_make_king_table.make_king_table_MOD_0_0}'
|
|
|
723 #end if
|
|
|
724
|
|
|
725 #if $str($CONDITIONAL_make_king_table.make_king_table_MOD_1_0):
|
|
|
726 '${CONDITIONAL_make_king_table.make_king_table_MOD_1_0}'
|
|
|
727 #end if
|
|
|
728
|
|
|
729 #if $str($CONDITIONAL_make_king_table.make_king_table_MOD_2_0):
|
|
|
730 '${CONDITIONAL_make_king_table.make_king_table_MOD_2_0}'
|
|
|
731 #end if
|
|
|
732
|
|
|
733 #if $str($CONDITIONAL_make_king_table.make_king_table_MOD_3_0):
|
|
|
734 '${CONDITIONAL_make_king_table.make_king_table_MOD_3_0}'
|
|
|
735 #end if
|
|
|
736
|
|
|
737 #end if
|
|
|
738
|
|
|
739 #if str($CONDITIONAL_make_rel.CONDITIONAL_SELECT_make_rel) == "set":
|
|
|
740 --make-rel
|
|
|
741
|
|
|
742
|
|
|
743 #if $str($CONDITIONAL_make_rel.make_rel_MOD_0_0):
|
|
|
744 '${CONDITIONAL_make_rel.make_rel_MOD_0_0}'
|
|
|
745 #end if
|
|
|
746
|
|
|
747 #if $str($CONDITIONAL_make_rel.make_rel_MOD_1_0):
|
|
|
748 '${CONDITIONAL_make_rel.make_rel_MOD_1_0}'
|
|
|
749 #end if
|
|
|
750
|
|
|
751 #if $str($CONDITIONAL_make_rel.CONDITIONAL_make_rel_MOD_2.CONDITIONAL_SELECT_make_rel_MOD_2) == 'from_list'
|
|
|
752 '${CONDITIONAL_make_rel.CONDITIONAL_make_rel_MOD_2.make_rel_MOD_2}'
|
|
|
753 #end if
|
|
|
754
|
|
|
755
|
|
|
756 #if $str($CONDITIONAL_make_rel.CONDITIONAL_make_rel_MOD_3.CONDITIONAL_SELECT_make_rel_MOD_3) == 'from_list'
|
|
|
757 '${CONDITIONAL_make_rel.CONDITIONAL_make_rel_MOD_3.make_rel_MOD_3}'
|
|
|
758 #end if
|
|
|
759
|
|
|
760
|
|
|
761 #end if
|
|
|
762
|
|
|
763 #if str($CONDITIONAL_make_grm_list.CONDITIONAL_SELECT_make_grm_list) == "set":
|
|
|
764 --make-grm-list
|
|
|
765
|
|
|
766
|
|
|
767 #if $str($CONDITIONAL_make_grm_list.make_grm_list_MOD_0_0):
|
|
|
768 '${CONDITIONAL_make_grm_list.make_grm_list_MOD_0_0}'
|
|
|
769 #end if
|
|
|
770
|
|
|
771 #if $str($CONDITIONAL_make_grm_list.make_grm_list_MOD_1_0):
|
|
|
772 '${CONDITIONAL_make_grm_list.make_grm_list_MOD_1_0}'
|
|
|
773 #end if
|
|
|
774
|
|
|
775 #if $str($CONDITIONAL_make_grm_list.make_grm_list_MOD_2_0):
|
|
|
776 '${CONDITIONAL_make_grm_list.make_grm_list_MOD_2_0}'
|
|
|
777 #end if
|
|
|
778
|
|
|
779 #if $str($CONDITIONAL_make_grm_list.CONDITIONAL_make_grm_list_MOD_3.CONDITIONAL_SELECT_make_grm_list_MOD_3) == 'from_list'
|
|
|
780 '${CONDITIONAL_make_grm_list.CONDITIONAL_make_grm_list_MOD_3.make_grm_list_MOD_3}'
|
|
|
781 #end if
|
|
|
782
|
|
|
783
|
|
|
784 #end if
|
|
|
785
|
|
|
786 #if str($CONDITIONAL_make_grm_bin.CONDITIONAL_SELECT_make_grm_bin) == "set":
|
|
|
787 --make-grm-bin
|
|
|
788
|
|
|
789
|
|
|
790 #if $str($CONDITIONAL_make_grm_bin.make_grm_bin_MOD_0_0):
|
|
|
791 '${CONDITIONAL_make_grm_bin.make_grm_bin_MOD_0_0}'
|
|
|
792 #end if
|
|
|
793
|
|
|
794 #if $str($CONDITIONAL_make_grm_bin.make_grm_bin_MOD_1_0):
|
|
|
795 '${CONDITIONAL_make_grm_bin.make_grm_bin_MOD_1_0}'
|
|
|
796 #end if
|
|
|
797
|
|
|
798 #if $str($CONDITIONAL_make_grm_bin.CONDITIONAL_make_grm_bin_MOD_2.CONDITIONAL_SELECT_make_grm_bin_MOD_2) == 'from_list'
|
|
|
799 '${CONDITIONAL_make_grm_bin.CONDITIONAL_make_grm_bin_MOD_2.make_grm_bin_MOD_2}'
|
|
|
800 #end if
|
|
|
801
|
|
|
802
|
|
|
803 #end if
|
|
|
804
|
|
|
805 #if str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_OVERLOADED_SELECT_pca) == "form_0":
|
|
|
806 #if str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_SELECT_pca) == "set":
|
|
|
807 --pca
|
|
|
808
|
|
|
809 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_0_0):
|
|
|
810 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_0_0}'
|
|
|
811 #end if
|
|
|
812 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_1.CONDITIONAL_SELECT_pca_MOD_1) == 'from_list'
|
|
|
813 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_1.pca_MOD_1}'
|
|
|
814 #end if
|
|
|
815
|
|
|
816 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_2_0):
|
|
|
817 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_2_0}'
|
|
|
818 #end if
|
|
|
819 #end if
|
|
|
820 #end if
|
|
|
821
|
|
|
822 #if str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_OVERLOADED_SELECT_pca) == "form_1":
|
|
|
823 #if str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_SELECT_pca) == "set":
|
|
|
824 --pca
|
|
|
825
|
|
|
826 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_0.CONDITIONAL_SELECT_pca_MOD_0) == 'from_list'
|
|
|
827 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_0.pca_MOD_0}'
|
|
|
828 #end if
|
|
|
829
|
|
|
830 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_1_0):
|
|
|
831 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_1_0}'
|
|
|
832 #end if
|
|
|
833 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_2.CONDITIONAL_SELECT_pca_MOD_2) == 'from_list'
|
|
|
834 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.CONDITIONAL_pca_MOD_2.pca_MOD_2}'
|
|
|
835 #end if
|
|
|
836
|
|
|
837 #if $str($CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_3_0):
|
|
|
838 '${CONDITIONAL_OVERLOADED_pca.CONDITIONAL_pca.pca_MOD_3_0}'
|
|
|
839 #end if
|
|
|
840 #end if
|
|
|
841 #end if
|
|
|
842
|
|
|
843 #if str($CONDITIONAL_king_cutoff.CONDITIONAL_SELECT_king_cutoff) == "set":
|
|
|
844 --king-cutoff
|
|
|
845
|
|
|
846
|
|
|
847 #if $str($CONDITIONAL_king_cutoff.king_cutoff_MOD_0_0):
|
|
|
848 '${CONDITIONAL_king_cutoff.king_cutoff_MOD_0_0}'
|
|
|
849 #end if
|
|
|
850
|
|
|
851 #if $str($CONDITIONAL_king_cutoff.king_cutoff_MOD_1_0):
|
|
|
852 '${CONDITIONAL_king_cutoff.king_cutoff_MOD_1_0}'
|
|
|
853 #end if
|
|
|
854
|
|
|
855 #end if
|
|
|
856
|
|
|
857 #if str($CONDITIONAL_write_covar.CONDITIONAL_SELECT_write_covar) == "set":
|
|
|
858 --write-covar
|
|
|
859
|
|
|
860
|
|
|
861 #if $str($CONDITIONAL_write_covar.write_covar_MOD_0_0):
|
|
|
862 '${CONDITIONAL_write_covar.write_covar_MOD_0_0}'
|
|
|
863 #end if
|
|
|
864
|
|
|
865 #end if
|
|
|
866
|
|
|
867 ${write_samples}
|
|
|
868
|
|
|
869 #if str($CONDITIONAL_write_snplist.CONDITIONAL_SELECT_write_snplist) == "set":
|
|
|
870 --write-snplist
|
|
|
871
|
|
|
872
|
|
|
873 #if $str($CONDITIONAL_write_snplist.write_snplist_MOD_0_0):
|
|
|
874 '${CONDITIONAL_write_snplist.write_snplist_MOD_0_0}'
|
|
|
875 #end if
|
|
|
876
|
|
|
877 #end if
|
|
|
878
|
|
|
879 #if str($CONDITIONAL_glm.CONDITIONAL_SELECT_glm) == "set":
|
|
|
880 --glm
|
|
|
881
|
|
|
882
|
|
|
883 #if $str($CONDITIONAL_glm.glm_MOD_0_0):
|
|
|
884 '${CONDITIONAL_glm.glm_MOD_0_0}'
|
|
|
885 #end if
|
|
|
886
|
|
|
887 #if $str($CONDITIONAL_glm.glm_MOD_1_0):
|
|
|
888 '${CONDITIONAL_glm.glm_MOD_1_0}'
|
|
|
889 #end if
|
|
|
890
|
|
|
891 #if $str($CONDITIONAL_glm.CONDITIONAL_glm_MOD_2.CONDITIONAL_SELECT_glm_MOD_2) == 'from_list'
|
|
|
892 '${CONDITIONAL_glm.CONDITIONAL_glm_MOD_2.glm_MOD_2}'
|
|
|
893 #end if
|
|
|
894
|
|
|
895
|
|
|
896 #if $str($CONDITIONAL_glm.glm_MOD_3_0):
|
|
|
897 '${CONDITIONAL_glm.glm_MOD_3_0}'
|
|
|
898 #end if
|
|
|
899
|
|
|
900 #if $str($CONDITIONAL_glm.glm_MOD_4_0):
|
|
|
901 '${CONDITIONAL_glm.glm_MOD_4_0}'
|
|
|
902 #end if
|
|
|
903
|
|
|
904 #end if
|
|
|
905
|
|
|
906 #if str($CONDITIONAL_score.CONDITIONAL_SELECT_score) == "set":
|
|
|
907 --score
|
|
|
908
|
|
|
909
|
|
|
910 #if $CONDITIONAL_score.score_MOD_0_0:
|
|
|
911 '${CONDITIONAL_score.score_MOD_0_0}'
|
|
|
912 #end if
|
|
|
913
|
|
|
914 #if $str($CONDITIONAL_score.score_MOD_1_0):
|
|
|
915 '${CONDITIONAL_score.score_MOD_1_0}'
|
|
|
916 #end if
|
|
|
917
|
|
|
918 #if $str($CONDITIONAL_score.score_MOD_2_0):
|
|
|
919 '${CONDITIONAL_score.score_MOD_2_0}'
|
|
|
920 #end if
|
|
|
921
|
|
|
922 #if $str($CONDITIONAL_score.score_MOD_3_0):
|
|
|
923 '${CONDITIONAL_score.score_MOD_3_0}'
|
|
|
924 #end if
|
|
|
925
|
|
|
926 #if $str($CONDITIONAL_score.CONDITIONAL_score_MOD_4.CONDITIONAL_SELECT_score_MOD_4) == 'from_list'
|
|
|
927 '${CONDITIONAL_score.CONDITIONAL_score_MOD_4.score_MOD_4}'
|
|
|
928 #end if
|
|
|
929
|
|
|
930
|
|
|
931 #if $str($CONDITIONAL_score.CONDITIONAL_score_MOD_5.CONDITIONAL_SELECT_score_MOD_5) == 'from_list'
|
|
|
932 '${CONDITIONAL_score.CONDITIONAL_score_MOD_5.score_MOD_5}'
|
|
|
933 #end if
|
|
|
934
|
|
|
935
|
|
|
936 #if $str($CONDITIONAL_score.score_MOD_6_0):
|
|
|
937 '${CONDITIONAL_score.score_MOD_6_0}'
|
|
|
938 #end if
|
|
|
939
|
|
|
940 #if $str($CONDITIONAL_score.score_MOD_7_0):
|
|
|
941 '${CONDITIONAL_score.score_MOD_7_0}'
|
|
|
942 #end if
|
|
|
943
|
|
|
944 #if $str($CONDITIONAL_score.score_MOD_8_0):
|
|
|
945 '${CONDITIONAL_score.score_MOD_8_0}'
|
|
|
946 #end if
|
|
|
947
|
|
|
948 #if $str($CONDITIONAL_score.score_MOD_9_0):
|
|
|
949 '${CONDITIONAL_score.score_MOD_9_0}'
|
|
|
950 #end if
|
|
|
951
|
|
|
952 #if $str($CONDITIONAL_score.CONDITIONAL_score_MOD_10.CONDITIONAL_SELECT_score_MOD_10) == 'from_list'
|
|
|
953 '${CONDITIONAL_score.CONDITIONAL_score_MOD_10.score_MOD_10}'
|
|
|
954 #end if
|
|
|
955
|
|
|
956
|
|
|
957 #if $str($CONDITIONAL_score.score_MOD_11_0):
|
|
|
958 '${CONDITIONAL_score.score_MOD_11_0}'
|
|
|
959 #end if
|
|
|
960
|
|
|
961 #end if
|
|
|
962
|
|
|
963 #if str($CONDITIONAL_variant_score.CONDITIONAL_SELECT_variant_score) == "set":
|
|
|
964 --variant-score
|
|
|
965
|
|
|
966
|
|
|
967 #if $CONDITIONAL_variant_score.variant_score_MOD_0_0:
|
|
|
968 '${CONDITIONAL_variant_score.variant_score_MOD_0_0}'
|
|
|
969 #end if
|
|
|
970
|
|
|
971 #if $str($CONDITIONAL_variant_score.variant_score_MOD_1_0):
|
|
|
972 '${CONDITIONAL_variant_score.variant_score_MOD_1_0}'
|
|
|
973 #end if
|
|
|
974
|
|
|
975 #if $str($CONDITIONAL_variant_score.CONDITIONAL_variant_score_MOD_2.CONDITIONAL_SELECT_variant_score_MOD_2) == 'from_list'
|
|
|
976 '${CONDITIONAL_variant_score.CONDITIONAL_variant_score_MOD_2.variant_score_MOD_2}'
|
|
|
977 #end if
|
|
|
978
|
|
|
979
|
|
|
980 #end if
|
|
|
981
|
|
|
982 #if str($CONDITIONAL_adjust_file.CONDITIONAL_SELECT_adjust_file) == "set":
|
|
|
983 --adjust-file
|
|
|
984
|
|
|
985
|
|
|
986 #if $CONDITIONAL_adjust_file.adjust_file_MOD_0_0:
|
|
|
987 '${CONDITIONAL_adjust_file.adjust_file_MOD_0_0}'
|
|
|
988 #end if
|
|
|
989
|
|
|
990 #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_1_0):
|
|
|
991 '${CONDITIONAL_adjust_file.adjust_file_MOD_1_0}'
|
|
|
992 #end if
|
|
|
993
|
|
|
994 #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_2_0):
|
|
|
995 '${CONDITIONAL_adjust_file.adjust_file_MOD_2_0}'
|
|
|
996 #end if
|
|
|
997
|
|
|
998 #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_3_0):
|
|
|
999 '${CONDITIONAL_adjust_file.adjust_file_MOD_3_0}'
|
|
|
1000 #end if
|
|
|
1001
|
|
|
1002 #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_4_0):
|
|
|
1003 '${CONDITIONAL_adjust_file.adjust_file_MOD_4_0}'
|
|
|
1004 #end if
|
|
|
1005
|
|
|
1006 #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_5_0):
|
|
|
1007 '${CONDITIONAL_adjust_file.adjust_file_MOD_5_0}'
|
|
|
1008 #end if
|
|
|
1009
|
|
|
1010 #if $str($CONDITIONAL_adjust_file.adjust_file_MOD_6_0):
|
|
|
1011 '${CONDITIONAL_adjust_file.adjust_file_MOD_6_0}'
|
|
|
1012 #end if
|
|
|
1013
|
|
|
1014 #end if
|
|
|
1015
|
|
|
1016 #if str($CONDITIONAL_genotyping_rate.CONDITIONAL_SELECT_genotyping_rate) == "set":
|
|
|
1017 --genotyping-rate
|
|
|
1018
|
|
|
1019
|
|
|
1020 #if $str($CONDITIONAL_genotyping_rate.genotyping_rate_MOD_0_0):
|
|
|
1021 '${CONDITIONAL_genotyping_rate.genotyping_rate_MOD_0_0}'
|
|
|
1022 #end if
|
|
|
1023
|
|
|
1024 #end if
|
|
|
1025
|
|
|
1026 ${pgen_info}
|
|
|
1027
|
|
|
1028 ${validate}
|
|
|
1029
|
|
|
1030 #if str($CONDITIONAL_zst_decompress.CONDITIONAL_SELECT_zst_decompress) == "set":
|
|
|
1031 --zst-decompress
|
|
|
1032
|
|
|
1033
|
|
|
1034 #if $str($CONDITIONAL_zst_decompress.zst_decompress_MOD_0_0):
|
|
|
1035 '${CONDITIONAL_zst_decompress.zst_decompress_MOD_0_0}'
|
|
|
1036 #end if
|
|
|
1037
|
|
|
1038 #if $str($CONDITIONAL_zst_decompress.zst_decompress_MOD_1_0):
|
|
|
1039 '${CONDITIONAL_zst_decompress.zst_decompress_MOD_1_0}'
|
|
|
1040 #end if
|
|
|
1041
|
|
|
1042 #end if
|
|
|
1043
|
|
|
1044 #if str($CONDITIONAL_silent.CONDITIONAL_SELECT_silent) == "set":
|
|
|
1045 --silent
|
|
|
1046
|
|
|
1047
|
|
|
1048 #end if
|
|
|
1049
|
|
|
1050 #if str($CONDITIONAL_double_id.CONDITIONAL_SELECT_double_id) == "set":
|
|
|
1051 --double-id
|
|
|
1052
|
|
|
1053
|
|
|
1054 #end if
|
|
|
1055
|
|
|
1056 #if str($CONDITIONAL_const_fid.CONDITIONAL_SELECT_const_fid) == "set":
|
|
|
1057 --const-fid
|
|
|
1058
|
|
|
1059
|
|
|
1060 #if $str($CONDITIONAL_const_fid.const_fid_MOD_0_0):
|
|
|
1061 '${CONDITIONAL_const_fid.const_fid_MOD_0_0}'
|
|
|
1062 #end if
|
|
|
1063
|
|
|
1064 #end if
|
|
|
1065
|
|
|
1066 #if str($CONDITIONAL_id_delim.CONDITIONAL_SELECT_id_delim) == "set":
|
|
|
1067 --id-delim
|
|
|
1068
|
|
|
1069
|
|
|
1070 #if $str($CONDITIONAL_id_delim.id_delim_MOD_0_0):
|
|
|
1071 '${CONDITIONAL_id_delim.id_delim_MOD_0_0}'
|
|
|
1072 #end if
|
|
|
1073
|
|
|
1074 #end if
|
|
|
1075
|
|
|
1076 #if str($CONDITIONAL_idspace_to.CONDITIONAL_SELECT_idspace_to) == "set":
|
|
|
1077 --idspace-to
|
|
|
1078
|
|
|
1079
|
|
|
1080 #if $str($CONDITIONAL_idspace_to.idspace_to_MOD_0_0):
|
|
|
1081 '${CONDITIONAL_idspace_to.idspace_to_MOD_0_0}'
|
|
|
1082 #end if
|
|
|
1083
|
|
|
1084 #end if
|
|
|
1085
|
|
|
1086 #if str($CONDITIONAL_iid_sid.CONDITIONAL_SELECT_iid_sid) == "set":
|
|
|
1087 --iid-sid
|
|
|
1088
|
|
|
1089
|
|
|
1090 #end if
|
|
|
1091
|
|
|
1092 #if str($CONDITIONAL_vcf_require_gt.CONDITIONAL_SELECT_vcf_require_gt) == "set":
|
|
|
1093 --vcf-require-gt
|
|
|
1094
|
|
|
1095
|
|
|
1096 #end if
|
|
|
1097
|
|
|
1098 #if str($CONDITIONAL_vcf_min_gq.CONDITIONAL_SELECT_vcf_min_gq) == "set":
|
|
|
1099 --vcf-min-gq
|
|
|
1100
|
|
|
1101
|
|
|
1102 #if $str($CONDITIONAL_vcf_min_gq.vcf_min_gq_MOD_0_0):
|
|
|
1103 '${CONDITIONAL_vcf_min_gq.vcf_min_gq_MOD_0_0}'
|
|
|
1104 #end if
|
|
|
1105
|
|
|
1106 #end if
|
|
|
1107
|
|
|
1108 #if str($CONDITIONAL_vcf_max_dp.CONDITIONAL_SELECT_vcf_max_dp) == "set":
|
|
|
1109 --vcf-max-dp
|
|
|
1110
|
|
|
1111
|
|
|
1112 #if $str($CONDITIONAL_vcf_max_dp.vcf_max_dp_MOD_0_0):
|
|
|
1113 '${CONDITIONAL_vcf_max_dp.vcf_max_dp_MOD_0_0}'
|
|
|
1114 #end if
|
|
|
1115
|
|
|
1116 #end if
|
|
|
1117
|
|
|
1118 #if str($CONDITIONAL_vcf_min_dp.CONDITIONAL_SELECT_vcf_min_dp) == "set":
|
|
|
1119 --vcf-min-dp
|
|
|
1120
|
|
|
1121
|
|
|
1122 #if $str($CONDITIONAL_vcf_min_dp.vcf_min_dp_MOD_0_0):
|
|
|
1123 '${CONDITIONAL_vcf_min_dp.vcf_min_dp_MOD_0_0}'
|
|
|
1124 #end if
|
|
|
1125
|
|
|
1126 #end if
|
|
|
1127
|
|
|
1128 #if str($CONDITIONAL_vcf_half_call.CONDITIONAL_SELECT_vcf_half_call) == "set":
|
|
|
1129 --vcf-half-call
|
|
|
1130
|
|
|
1131
|
|
|
1132 #if $str($CONDITIONAL_vcf_half_call.vcf_half_call_MOD_0_0):
|
|
|
1133 '${CONDITIONAL_vcf_half_call.vcf_half_call_MOD_0_0}'
|
|
|
1134 #end if
|
|
|
1135
|
|
|
1136 #end if
|
|
|
1137
|
|
|
1138 #if str($CONDITIONAL_oxford_single_chr.CONDITIONAL_SELECT_oxford_single_chr) == "set":
|
|
|
1139 --oxford-single-chr
|
|
|
1140
|
|
|
1141
|
|
|
1142 #if $str($CONDITIONAL_oxford_single_chr.oxford_single_chr_MOD_0_0):
|
|
|
1143 '${CONDITIONAL_oxford_single_chr.oxford_single_chr_MOD_0_0}'
|
|
|
1144 #end if
|
|
|
1145
|
|
|
1146 #end if
|
|
|
1147
|
|
|
1148 #if str($CONDITIONAL_missing_code.CONDITIONAL_SELECT_missing_code) == "set":
|
|
|
1149 --missing-code
|
|
|
1150
|
|
|
1151
|
|
|
1152 #if $str($CONDITIONAL_missing_code.missing_code_MOD_0_0):
|
|
|
1153 '${CONDITIONAL_missing_code.missing_code_MOD_0_0}'
|
|
|
1154 #end if
|
|
|
1155
|
|
|
1156 #end if
|
|
|
1157
|
|
|
1158 #if str($CONDITIONAL_hard_call_threshold.CONDITIONAL_SELECT_hard_call_threshold) == "set":
|
|
|
1159 --hard-call-threshold
|
|
|
1160
|
|
|
1161
|
|
|
1162 #if $str($CONDITIONAL_hard_call_threshold.hard_call_threshold_MOD_0_0):
|
|
|
1163 '${CONDITIONAL_hard_call_threshold.hard_call_threshold_MOD_0_0}'
|
|
|
1164 #end if
|
|
|
1165
|
|
|
1166 #end if
|
|
|
1167
|
|
|
1168 #if str($CONDITIONAL_dosage_erase_threshold.CONDITIONAL_SELECT_dosage_erase_threshold) == "set":
|
|
|
1169 --dosage-erase-threshold
|
|
|
1170
|
|
|
1171
|
|
|
1172 #if $str($CONDITIONAL_dosage_erase_threshold.dosage_erase_threshold_MOD_0_0):
|
|
|
1173 '${CONDITIONAL_dosage_erase_threshold.dosage_erase_threshold_MOD_0_0}'
|
|
|
1174 #end if
|
|
|
1175
|
|
|
1176 #end if
|
|
|
1177
|
|
|
1178 #if str($CONDITIONAL_import_dosage_certainty.CONDITIONAL_SELECT_import_dosage_certainty) == "set":
|
|
|
1179 --import-dosage-certainty
|
|
|
1180
|
|
|
1181
|
|
|
1182 #if $str($CONDITIONAL_import_dosage_certainty.import_dosage_certainty_MOD_0_0):
|
|
|
1183 '${CONDITIONAL_import_dosage_certainty.import_dosage_certainty_MOD_0_0}'
|
|
|
1184 #end if
|
|
|
1185
|
|
|
1186 #end if
|
|
|
1187
|
|
|
1188 #if str($CONDITIONAL_input_missing_genotype.CONDITIONAL_SELECT_input_missing_genotype) == "set":
|
|
|
1189 --input-missing-genotype
|
|
|
1190
|
|
|
1191
|
|
|
1192 #if $str($CONDITIONAL_input_missing_genotype.input_missing_genotype_MOD_0_0):
|
|
|
1193 '${CONDITIONAL_input_missing_genotype.input_missing_genotype_MOD_0_0}'
|
|
|
1194 #end if
|
|
|
1195
|
|
|
1196 #end if
|
|
|
1197
|
|
|
1198 #if str($CONDITIONAL_allow_extra_chr.CONDITIONAL_SELECT_allow_extra_chr) == "set":
|
|
|
1199 --allow-extra-chr
|
|
|
1200
|
|
|
1201
|
|
|
1202 #end if
|
|
|
1203
|
|
|
1204 #if str($CONDITIONAL_chr_set.CONDITIONAL_SELECT_chr_set) == "set":
|
|
|
1205 --chr-set
|
|
|
1206
|
|
|
1207
|
|
|
1208 #if $str($CONDITIONAL_chr_set.chr_set_MOD_0_0):
|
|
|
1209 '${CONDITIONAL_chr_set.chr_set_MOD_0_0}'
|
|
|
1210 #end if
|
|
|
1211
|
|
|
1212 #if $str($CONDITIONAL_chr_set.chr_set_MOD_1_0):
|
|
|
1213 '${CONDITIONAL_chr_set.chr_set_MOD_1_0}'
|
|
|
1214 #end if
|
|
|
1215
|
|
|
1216 #if $str($CONDITIONAL_chr_set.chr_set_MOD_2_0):
|
|
|
1217 '${CONDITIONAL_chr_set.chr_set_MOD_2_0}'
|
|
|
1218 #end if
|
|
|
1219
|
|
|
1220 #if $str($CONDITIONAL_chr_set.chr_set_MOD_3_0):
|
|
|
1221 '${CONDITIONAL_chr_set.chr_set_MOD_3_0}'
|
|
|
1222 #end if
|
|
|
1223
|
|
|
1224 #if $str($CONDITIONAL_chr_set.chr_set_MOD_4_0):
|
|
|
1225 '${CONDITIONAL_chr_set.chr_set_MOD_4_0}'
|
|
|
1226 #end if
|
|
|
1227
|
|
|
1228 #end if
|
|
|
1229
|
|
|
1230 #if str($CONDITIONAL_cow.CONDITIONAL_SELECT_cow) == "set":
|
|
|
1231 --cow
|
|
|
1232
|
|
|
1233
|
|
|
1234 #end if
|
|
|
1235
|
|
|
1236 #if str($CONDITIONAL_dog.CONDITIONAL_SELECT_dog) == "set":
|
|
|
1237 --dog
|
|
|
1238
|
|
|
1239
|
|
|
1240 #end if
|
|
|
1241
|
|
|
1242 #if str($CONDITIONAL_horse.CONDITIONAL_SELECT_horse) == "set":
|
|
|
1243 --horse
|
|
|
1244
|
|
|
1245
|
|
|
1246 #end if
|
|
|
1247
|
|
|
1248 #if str($CONDITIONAL_mouse.CONDITIONAL_SELECT_mouse) == "set":
|
|
|
1249 --mouse
|
|
|
1250
|
|
|
1251
|
|
|
1252 #end if
|
|
|
1253
|
|
|
1254 #if str($CONDITIONAL_rice.CONDITIONAL_SELECT_rice) == "set":
|
|
|
1255 --rice
|
|
|
1256
|
|
|
1257
|
|
|
1258 #end if
|
|
|
1259
|
|
|
1260 #if str($CONDITIONAL_sheep.CONDITIONAL_SELECT_sheep) == "set":
|
|
|
1261 --sheep
|
|
|
1262
|
|
|
1263
|
|
|
1264 #end if
|
|
|
1265
|
|
|
1266 #if str($CONDITIONAL_autosome_num.CONDITIONAL_SELECT_autosome_num) == "set":
|
|
|
1267 --autosome-num
|
|
|
1268
|
|
|
1269
|
|
|
1270 #if $str($CONDITIONAL_autosome_num.autosome_num_MOD_0_0):
|
|
|
1271 '${CONDITIONAL_autosome_num.autosome_num_MOD_0_0}'
|
|
|
1272 #end if
|
|
|
1273
|
|
|
1274 #end if
|
|
|
1275
|
|
|
1276 #if str($CONDITIONAL_human.CONDITIONAL_SELECT_human) == "set":
|
|
|
1277 --human
|
|
|
1278
|
|
|
1279
|
|
|
1280 #end if
|
|
|
1281
|
|
|
1282 #if str($CONDITIONAL_chr_override.CONDITIONAL_SELECT_chr_override) == "set":
|
|
|
1283 --chr-override
|
|
|
1284
|
|
|
1285
|
|
|
1286 #if $str($CONDITIONAL_chr_override.chr_override_MOD_0_0):
|
|
|
1287 '${CONDITIONAL_chr_override.chr_override_MOD_0_0}'
|
|
|
1288 #end if
|
|
|
1289
|
|
|
1290 #end if
|
|
|
1291
|
|
|
1292 #if str($CONDITIONAL_var_min_qual.CONDITIONAL_SELECT_var_min_qual) == "set":
|
|
|
1293 --var-min-qual
|
|
|
1294
|
|
|
1295
|
|
|
1296 #if $str($CONDITIONAL_var_min_qual.var_min_qual_MOD_0_0):
|
|
|
1297 '${CONDITIONAL_var_min_qual.var_min_qual_MOD_0_0}'
|
|
|
1298 #end if
|
|
|
1299
|
|
|
1300 #end if
|
|
|
1301
|
|
|
1302 #if str($CONDITIONAL_var_filter.CONDITIONAL_SELECT_var_filter) == "set":
|
|
|
1303 --var-filter
|
|
|
1304
|
|
|
1305
|
|
|
1306 #if $str($CONDITIONAL_var_filter.var_filter_MOD_0_0):
|
|
|
1307 '${CONDITIONAL_var_filter.var_filter_MOD_0_0}'
|
|
|
1308 #end if
|
|
|
1309
|
|
|
1310 #end if
|
|
|
1311
|
|
|
1312 #if str($CONDITIONAL_extract_if_info.CONDITIONAL_SELECT_extract_if_info) == "set":
|
|
|
1313 --extract-if-info
|
|
|
1314
|
|
|
1315
|
|
|
1316 #if $str($CONDITIONAL_extract_if_info.extract_if_info_MOD_0_0):
|
|
|
1317 '${CONDITIONAL_extract_if_info.extract_if_info_MOD_0_0}'
|
|
|
1318 #end if
|
|
|
1319
|
|
|
1320 #if $str($CONDITIONAL_extract_if_info.extract_if_info_MOD_1_0):
|
|
|
1321 '${CONDITIONAL_extract_if_info.extract_if_info_MOD_1_0}'
|
|
|
1322 #end if
|
|
|
1323
|
|
|
1324 #if $str($CONDITIONAL_extract_if_info.extract_if_info_MOD_2_0):
|
|
|
1325 '${CONDITIONAL_extract_if_info.extract_if_info_MOD_2_0}'
|
|
|
1326 #end if
|
|
|
1327
|
|
|
1328 #end if
|
|
|
1329
|
|
|
1330 #if str($CONDITIONAL_exclude_if_info.CONDITIONAL_SELECT_exclude_if_info) == "set":
|
|
|
1331 --exclude-if-info
|
|
|
1332
|
|
|
1333
|
|
|
1334 #if $str($CONDITIONAL_exclude_if_info.exclude_if_info_MOD_0_0):
|
|
|
1335 '${CONDITIONAL_exclude_if_info.exclude_if_info_MOD_0_0}'
|
|
|
1336 #end if
|
|
|
1337
|
|
|
1338 #if $str($CONDITIONAL_exclude_if_info.exclude_if_info_MOD_1_0):
|
|
|
1339 '${CONDITIONAL_exclude_if_info.exclude_if_info_MOD_1_0}'
|
|
|
1340 #end if
|
|
|
1341
|
|
|
1342 #if $str($CONDITIONAL_exclude_if_info.exclude_if_info_MOD_2_0):
|
|
|
1343 '${CONDITIONAL_exclude_if_info.exclude_if_info_MOD_2_0}'
|
|
|
1344 #end if
|
|
|
1345
|
|
|
1346 #end if
|
|
|
1347
|
|
|
1348 #if str($CONDITIONAL_require_info.CONDITIONAL_SELECT_require_info) == "set":
|
|
|
1349 --require-info
|
|
|
1350
|
|
|
1351
|
|
|
1352 #if $str($CONDITIONAL_require_info.require_info_MOD_0_0):
|
|
|
1353 '${CONDITIONAL_require_info.require_info_MOD_0_0}'
|
|
|
1354 #end if
|
|
|
1355
|
|
|
1356 #end if
|
|
|
1357
|
|
|
1358 #if str($CONDITIONAL_require_no_info.CONDITIONAL_SELECT_require_no_info) == "set":
|
|
|
1359 --require-no-info
|
|
|
1360
|
|
|
1361
|
|
|
1362 #if $str($CONDITIONAL_require_no_info.require_no_info_MOD_0_0):
|
|
|
1363 '${CONDITIONAL_require_no_info.require_no_info_MOD_0_0}'
|
|
|
1364 #end if
|
|
|
1365
|
|
|
1366 #if $str($CONDITIONAL_require_no_info.require_no_info_MOD_1_0):
|
|
|
1367 '${CONDITIONAL_require_no_info.require_no_info_MOD_1_0}'
|
|
|
1368 #end if
|
|
|
1369
|
|
|
1370 #end if
|
|
|
1371
|
|
|
1372 #if str($CONDITIONAL_extract_col_cond.CONDITIONAL_SELECT_extract_col_cond) == "set":
|
|
|
1373 --extract-col-cond
|
|
|
1374
|
|
|
1375
|
|
|
1376 #if $CONDITIONAL_extract_col_cond.extract_col_cond_MOD_0_0:
|
|
|
1377 '${CONDITIONAL_extract_col_cond.extract_col_cond_MOD_0_0}'
|
|
|
1378 #end if
|
|
|
1379
|
|
|
1380 #if $str($CONDITIONAL_extract_col_cond.extract_col_cond_MOD_1_0):
|
|
|
1381 '${CONDITIONAL_extract_col_cond.extract_col_cond_MOD_1_0}'
|
|
|
1382 #end if
|
|
|
1383
|
|
|
1384 #if $str($CONDITIONAL_extract_col_cond.extract_col_cond_MOD_2_0):
|
|
|
1385 '${CONDITIONAL_extract_col_cond.extract_col_cond_MOD_2_0}'
|
|
|
1386 #end if
|
|
|
1387
|
|
|
1388 #if $str($CONDITIONAL_extract_col_cond.extract_col_cond_MOD_3_0):
|
|
|
1389 '${CONDITIONAL_extract_col_cond.extract_col_cond_MOD_3_0}'
|
|
|
1390 #end if
|
|
|
1391
|
|
|
1392 #end if
|
|
|
1393
|
|
|
1394 #if str($CONDITIONAL_extract_col_cond_match.CONDITIONAL_SELECT_extract_col_cond_match) == "set":
|
|
|
1395 --extract-col-cond-match
|
|
|
1396
|
|
|
1397
|
|
|
1398 #if $str($CONDITIONAL_extract_col_cond_match.extract_col_cond_match_MOD_0_0):
|
|
|
1399 '${CONDITIONAL_extract_col_cond_match.extract_col_cond_match_MOD_0_0}'
|
|
|
1400 #end if
|
|
|
1401
|
|
|
1402 #end if
|
|
|
1403
|
|
|
1404 #if str($CONDITIONAL_extract_col_cond_mismatch.CONDITIONAL_SELECT_extract_col_cond_mismatch) == "set":
|
|
|
1405 --extract-col-cond-mismatch
|
|
|
1406
|
|
|
1407
|
|
|
1408 #if $str($CONDITIONAL_extract_col_cond_mismatch.extract_col_cond_mismatch_MOD_0_0):
|
|
|
1409 '${CONDITIONAL_extract_col_cond_mismatch.extract_col_cond_mismatch_MOD_0_0}'
|
|
|
1410 #end if
|
|
|
1411
|
|
|
1412 #end if
|
|
|
1413
|
|
|
1414 ${extract_col_cond_substr}
|
|
|
1415
|
|
|
1416 #if str($CONDITIONAL_extract_col_cond_min.CONDITIONAL_SELECT_extract_col_cond_min) == "set":
|
|
|
1417 --extract-col-cond-min
|
|
|
1418
|
|
|
1419
|
|
|
1420 #if $str($CONDITIONAL_extract_col_cond_min.extract_col_cond_min_MOD_0_0):
|
|
|
1421 '${CONDITIONAL_extract_col_cond_min.extract_col_cond_min_MOD_0_0}'
|
|
|
1422 #end if
|
|
|
1423
|
|
|
1424 #end if
|
|
|
1425
|
|
|
1426 #if str($CONDITIONAL_extract_col_cond_max.CONDITIONAL_SELECT_extract_col_cond_max) == "set":
|
|
|
1427 --extract-col-cond-max
|
|
|
1428
|
|
|
1429
|
|
|
1430 #if $str($CONDITIONAL_extract_col_cond_max.extract_col_cond_max_MOD_0_0):
|
|
|
1431 '${CONDITIONAL_extract_col_cond_max.extract_col_cond_max_MOD_0_0}'
|
|
|
1432 #end if
|
|
|
1433
|
|
|
1434 #end if
|
|
|
1435
|
|
|
1436 #if str($CONDITIONAL_pheno.CONDITIONAL_SELECT_pheno) == "set":
|
|
|
1437 --pheno
|
|
|
1438
|
|
|
1439
|
|
|
1440 #if $str($CONDITIONAL_pheno.pheno_MOD_0_0):
|
|
|
1441 '${CONDITIONAL_pheno.pheno_MOD_0_0}'
|
|
|
1442 #end if
|
|
|
1443
|
|
|
1444 #if $CONDITIONAL_pheno.pheno_MOD_1_0:
|
|
|
1445 '${CONDITIONAL_pheno.pheno_MOD_1_0}'
|
|
|
1446 #end if
|
|
|
1447
|
|
|
1448 #end if
|
|
|
1449
|
|
|
1450 #if str($CONDITIONAL_pheno_name.CONDITIONAL_SELECT_pheno_name) == "set":
|
|
|
1451 --pheno-name
|
|
|
1452
|
|
|
1453
|
|
|
1454 #if $str($CONDITIONAL_pheno_name.pheno_name_MOD_0_0):
|
|
|
1455 '${CONDITIONAL_pheno_name.pheno_name_MOD_0_0}'
|
|
|
1456 #end if
|
|
|
1457
|
|
|
1458 #end if
|
|
|
1459
|
|
|
1460 #if str($CONDITIONAL_pheno_col_nums.CONDITIONAL_SELECT_pheno_col_nums) == "set":
|
|
|
1461 --pheno-col-nums
|
|
|
1462
|
|
|
1463
|
|
|
1464 #if $str($CONDITIONAL_pheno_col_nums.pheno_col_nums_MOD_0_0):
|
|
|
1465 '${CONDITIONAL_pheno_col_nums.pheno_col_nums_MOD_0_0}'
|
|
|
1466 #end if
|
|
|
1467
|
|
|
1468 #end if
|
|
|
1469
|
|
|
1470 #if str($CONDITIONAL_no_psam_pheno.CONDITIONAL_SELECT_no_psam_pheno) == "set":
|
|
|
1471 --no-psam-pheno
|
|
|
1472
|
|
|
1473
|
|
|
1474 #end if
|
|
|
1475
|
|
|
1476 #if str($CONDITIONAL_strict_sid0.CONDITIONAL_SELECT_strict_sid0) == "set":
|
|
|
1477 --strict-sid0
|
|
|
1478
|
|
|
1479
|
|
|
1480 #end if
|
|
|
1481
|
|
|
1482 #if str($CONDITIONAL_input_missing_phenotype.CONDITIONAL_SELECT_input_missing_phenotype) == "set":
|
|
|
1483 --input-missing-phenotype
|
|
|
1484
|
|
|
1485
|
|
|
1486 #if $str($CONDITIONAL_input_missing_phenotype.input_missing_phenotype_MOD_0_0):
|
|
|
1487 '${CONDITIONAL_input_missing_phenotype.input_missing_phenotype_MOD_0_0}'
|
|
|
1488 #end if
|
|
|
1489
|
|
|
1490 #end if
|
|
|
1491
|
|
|
1492 #if str($CONDITIONAL_no_input_missing_phenotype.CONDITIONAL_SELECT_no_input_missing_phenotype) == "set":
|
|
|
1493 --no-input-missing-phenotype
|
|
|
1494
|
|
|
1495
|
|
|
1496 #end if
|
|
|
1497
|
|
|
1498 #if str($CONDITIONAL_GALAXY_1.CONDITIONAL_SELECT_GALAXY_1) == "set":
|
|
|
1499 --1
|
|
|
1500
|
|
|
1501
|
|
|
1502 #end if
|
|
|
1503
|
|
|
1504 #if str($CONDITIONAL_missing_catname.CONDITIONAL_SELECT_missing_catname) == "set":
|
|
|
1505 --missing-catname
|
|
|
1506
|
|
|
1507
|
|
|
1508 #if $str($CONDITIONAL_missing_catname.missing_catname_MOD_0_0):
|
|
|
1509 '${CONDITIONAL_missing_catname.missing_catname_MOD_0_0}'
|
|
|
1510 #end if
|
|
|
1511
|
|
|
1512 #end if
|
|
|
1513
|
|
|
1514 #if str($CONDITIONAL_covar.CONDITIONAL_SELECT_covar) == "set":
|
|
|
1515 --covar
|
|
|
1516
|
|
|
1517
|
|
|
1518 #if $str($CONDITIONAL_covar.covar_MOD_0_0):
|
|
|
1519 '${CONDITIONAL_covar.covar_MOD_0_0}'
|
|
|
1520 #end if
|
|
|
1521
|
|
|
1522 #if $CONDITIONAL_covar.covar_MOD_1_0:
|
|
|
1523 '${CONDITIONAL_covar.covar_MOD_1_0}'
|
|
|
1524 #end if
|
|
|
1525
|
|
|
1526 #end if
|
|
|
1527
|
|
|
1528 #if str($CONDITIONAL_covar_name.CONDITIONAL_SELECT_covar_name) == "set":
|
|
|
1529 --covar-name
|
|
|
1530
|
|
|
1531
|
|
|
1532 #if $str($CONDITIONAL_covar_name.covar_name_MOD_0_0):
|
|
|
1533 '${CONDITIONAL_covar_name.covar_name_MOD_0_0}'
|
|
|
1534 #end if
|
|
|
1535
|
|
|
1536 #end if
|
|
|
1537
|
|
|
1538 #if str($CONDITIONAL_covar_col_nums.CONDITIONAL_SELECT_covar_col_nums) == "set":
|
|
|
1539 --covar-col-nums
|
|
|
1540
|
|
|
1541
|
|
|
1542 #if $str($CONDITIONAL_covar_col_nums.covar_col_nums_MOD_0_0):
|
|
|
1543 '${CONDITIONAL_covar_col_nums.covar_col_nums_MOD_0_0}'
|
|
|
1544 #end if
|
|
|
1545
|
|
|
1546 #end if
|
|
|
1547
|
|
|
1548 #if str($CONDITIONAL_within.CONDITIONAL_SELECT_within) == "set":
|
|
|
1549 --within
|
|
|
1550
|
|
|
1551
|
|
|
1552 #if $CONDITIONAL_within.within_MOD_0_0:
|
|
|
1553 '${CONDITIONAL_within.within_MOD_0_0}'
|
|
|
1554 #end if
|
|
|
1555
|
|
|
1556 #if $str($CONDITIONAL_within.within_MOD_1_0):
|
|
|
1557 '${CONDITIONAL_within.within_MOD_1_0}'
|
|
|
1558 #end if
|
|
|
1559
|
|
|
1560 #end if
|
|
|
1561
|
|
|
1562 #if str($CONDITIONAL_mwithin.CONDITIONAL_SELECT_mwithin) == "set":
|
|
|
1563 --mwithin
|
|
|
1564
|
|
|
1565
|
|
|
1566 #if $str($CONDITIONAL_mwithin.mwithin_MOD_0_0):
|
|
|
1567 '${CONDITIONAL_mwithin.mwithin_MOD_0_0}'
|
|
|
1568 #end if
|
|
|
1569
|
|
|
1570 #end if
|
|
|
1571
|
|
|
1572 #if str($CONDITIONAL_family.CONDITIONAL_SELECT_family) == "set":
|
|
|
1573 --family
|
|
|
1574
|
|
|
1575
|
|
|
1576 #if $str($CONDITIONAL_family.family_MOD_0_0):
|
|
|
1577 '${CONDITIONAL_family.family_MOD_0_0}'
|
|
|
1578 #end if
|
|
|
1579
|
|
|
1580 #end if
|
|
|
1581
|
|
|
1582 #if str($CONDITIONAL_family_missing_catname.CONDITIONAL_SELECT_family_missing_catname) == "set":
|
|
|
1583 --family-missing-catname
|
|
|
1584
|
|
|
1585
|
|
|
1586 #if $str($CONDITIONAL_family_missing_catname.family_missing_catname_MOD_0_0):
|
|
|
1587 '${CONDITIONAL_family_missing_catname.family_missing_catname_MOD_0_0}'
|
|
|
1588 #end if
|
|
|
1589
|
|
|
1590 #end if
|
|
|
1591
|
|
|
1592 #if str($CONDITIONAL_keep.CONDITIONAL_SELECT_keep) == "set":
|
|
|
1593 --keep
|
|
|
1594
|
|
|
1595
|
|
|
1596 #if $str($CONDITIONAL_keep.keep_MOD_0_0):
|
|
|
1597 '${CONDITIONAL_keep.keep_MOD_0_0}'
|
|
|
1598 #end if
|
|
|
1599
|
|
|
1600 #end if
|
|
|
1601
|
|
|
1602 #if str($CONDITIONAL_remove.CONDITIONAL_SELECT_remove) == "set":
|
|
|
1603 --remove
|
|
|
1604
|
|
|
1605
|
|
|
1606 #if $str($CONDITIONAL_remove.remove_MOD_0_0):
|
|
|
1607 '${CONDITIONAL_remove.remove_MOD_0_0}'
|
|
|
1608 #end if
|
|
|
1609
|
|
|
1610 #end if
|
|
|
1611
|
|
|
1612 #if str($CONDITIONAL_keep_fam.CONDITIONAL_SELECT_keep_fam) == "set":
|
|
|
1613 --keep-fam
|
|
|
1614
|
|
|
1615
|
|
|
1616 #if $str($CONDITIONAL_keep_fam.keep_fam_MOD_0_0):
|
|
|
1617 '${CONDITIONAL_keep_fam.keep_fam_MOD_0_0}'
|
|
|
1618 #end if
|
|
|
1619
|
|
|
1620 #end if
|
|
|
1621
|
|
|
1622 #if str($CONDITIONAL_remove_fam.CONDITIONAL_SELECT_remove_fam) == "set":
|
|
|
1623 --remove-fam
|
|
|
1624
|
|
|
1625
|
|
|
1626 #if $str($CONDITIONAL_remove_fam.remove_fam_MOD_0_0):
|
|
|
1627 '${CONDITIONAL_remove_fam.remove_fam_MOD_0_0}'
|
|
|
1628 #end if
|
|
|
1629
|
|
|
1630 #end if
|
|
|
1631
|
|
|
1632 #if str($CONDITIONAL_extract.CONDITIONAL_SELECT_extract) == "set":
|
|
|
1633 --extract
|
|
|
1634
|
|
|
1635
|
|
|
1636 #if $str($CONDITIONAL_extract.CONDITIONAL_extract_MOD_0.CONDITIONAL_SELECT_extract_MOD_0) == 'from_list'
|
|
|
1637 '${CONDITIONAL_extract.CONDITIONAL_extract_MOD_0.extract_MOD_0}'
|
|
|
1638 #end if
|
|
|
1639
|
|
|
1640
|
|
|
1641 #if $str($CONDITIONAL_extract.extract_MOD_1_0):
|
|
|
1642 '${CONDITIONAL_extract.extract_MOD_1_0}'
|
|
|
1643 #end if
|
|
|
1644
|
|
|
1645 #end if
|
|
|
1646
|
|
|
1647 #if str($CONDITIONAL_exclude.CONDITIONAL_SELECT_exclude) == "set":
|
|
|
1648 --exclude
|
|
|
1649
|
|
|
1650
|
|
|
1651 #if $str($CONDITIONAL_exclude.CONDITIONAL_exclude_MOD_0.CONDITIONAL_SELECT_exclude_MOD_0) == 'from_list'
|
|
|
1652 '${CONDITIONAL_exclude.CONDITIONAL_exclude_MOD_0.exclude_MOD_0}'
|
|
|
1653 #end if
|
|
|
1654
|
|
|
1655
|
|
|
1656 #if $str($CONDITIONAL_exclude.exclude_MOD_1_0):
|
|
|
1657 '${CONDITIONAL_exclude.exclude_MOD_1_0}'
|
|
|
1658 #end if
|
|
|
1659
|
|
|
1660 #end if
|
|
|
1661
|
|
|
1662 #if str($CONDITIONAL_extract_intersect.CONDITIONAL_SELECT_extract_intersect) == "set":
|
|
|
1663 --extract-intersect
|
|
|
1664
|
|
|
1665
|
|
|
1666 #if $str($CONDITIONAL_extract_intersect.CONDITIONAL_extract_intersect_MOD_0.CONDITIONAL_SELECT_extract_intersect_MOD_0) == 'from_list'
|
|
|
1667 '${CONDITIONAL_extract_intersect.CONDITIONAL_extract_intersect_MOD_0.extract_intersect_MOD_0}'
|
|
|
1668 #end if
|
|
|
1669
|
|
|
1670
|
|
|
1671 #if $str($CONDITIONAL_extract_intersect.extract_intersect_MOD_1_0):
|
|
|
1672 '${CONDITIONAL_extract_intersect.extract_intersect_MOD_1_0}'
|
|
|
1673 #end if
|
|
|
1674
|
|
|
1675 #end if
|
|
|
1676
|
|
|
1677 #if str($CONDITIONAL_keep_cats.CONDITIONAL_SELECT_keep_cats) == "set":
|
|
|
1678 --keep-cats
|
|
|
1679
|
|
|
1680
|
|
|
1681 #if $CONDITIONAL_keep_cats.keep_cats_MOD_0_0:
|
|
|
1682 '${CONDITIONAL_keep_cats.keep_cats_MOD_0_0}'
|
|
|
1683 #end if
|
|
|
1684
|
|
|
1685 #end if
|
|
|
1686
|
|
|
1687 #if str($CONDITIONAL_keep_cat_names.CONDITIONAL_SELECT_keep_cat_names) == "set":
|
|
|
1688 --keep-cat-names
|
|
|
1689
|
|
|
1690
|
|
|
1691 #if $str($CONDITIONAL_keep_cat_names.keep_cat_names_MOD_0_0):
|
|
|
1692 '${CONDITIONAL_keep_cat_names.keep_cat_names_MOD_0_0}'
|
|
|
1693 #end if
|
|
|
1694
|
|
|
1695 #end if
|
|
|
1696
|
|
|
1697 #if str($CONDITIONAL_keep_cat_pheno.CONDITIONAL_SELECT_keep_cat_pheno) == "set":
|
|
|
1698 --keep-cat-pheno
|
|
|
1699
|
|
|
1700
|
|
|
1701 #if $str($CONDITIONAL_keep_cat_pheno.keep_cat_pheno_MOD_0_0):
|
|
|
1702 '${CONDITIONAL_keep_cat_pheno.keep_cat_pheno_MOD_0_0}'
|
|
|
1703 #end if
|
|
|
1704
|
|
|
1705 #end if
|
|
|
1706
|
|
|
1707 #if str($CONDITIONAL_remove_cats.CONDITIONAL_SELECT_remove_cats) == "set":
|
|
|
1708 --remove-cats
|
|
|
1709
|
|
|
1710
|
|
|
1711 #if $CONDITIONAL_remove_cats.remove_cats_MOD_0_0:
|
|
|
1712 '${CONDITIONAL_remove_cats.remove_cats_MOD_0_0}'
|
|
|
1713 #end if
|
|
|
1714
|
|
|
1715 #end if
|
|
|
1716
|
|
|
1717 #if str($CONDITIONAL_remove_cat_names.CONDITIONAL_SELECT_remove_cat_names) == "set":
|
|
|
1718 --remove-cat-names
|
|
|
1719
|
|
|
1720
|
|
|
1721 #if $str($CONDITIONAL_remove_cat_names.remove_cat_names_MOD_0_0):
|
|
|
1722 '${CONDITIONAL_remove_cat_names.remove_cat_names_MOD_0_0}'
|
|
|
1723 #end if
|
|
|
1724
|
|
|
1725 #end if
|
|
|
1726
|
|
|
1727 #if str($CONDITIONAL_remove_cat_pheno.CONDITIONAL_SELECT_remove_cat_pheno) == "set":
|
|
|
1728 --remove-cat-pheno
|
|
|
1729
|
|
|
1730
|
|
|
1731 #if $str($CONDITIONAL_remove_cat_pheno.remove_cat_pheno_MOD_0_0):
|
|
|
1732 '${CONDITIONAL_remove_cat_pheno.remove_cat_pheno_MOD_0_0}'
|
|
|
1733 #end if
|
|
|
1734
|
|
|
1735 #end if
|
|
|
1736
|
|
|
1737 #if str($CONDITIONAL_split_cat_pheno.CONDITIONAL_SELECT_split_cat_pheno) == "set":
|
|
|
1738 --split-cat-pheno
|
|
|
1739
|
|
|
1740
|
|
|
1741 #if $str($CONDITIONAL_split_cat_pheno.CONDITIONAL_split_cat_pheno_MOD_0.CONDITIONAL_SELECT_split_cat_pheno_MOD_0) == 'from_list'
|
|
|
1742 '${CONDITIONAL_split_cat_pheno.CONDITIONAL_split_cat_pheno_MOD_0.split_cat_pheno_MOD_0}'
|
|
|
1743 #end if
|
|
|
1744
|
|
|
1745
|
|
|
1746 #if $str($CONDITIONAL_split_cat_pheno.split_cat_pheno_MOD_1_0):
|
|
|
1747 '${CONDITIONAL_split_cat_pheno.split_cat_pheno_MOD_1_0}'
|
|
|
1748 #end if
|
|
|
1749
|
|
|
1750 #if $str($CONDITIONAL_split_cat_pheno.split_cat_pheno_MOD_2_0):
|
|
|
1751 '${CONDITIONAL_split_cat_pheno.split_cat_pheno_MOD_2_0}'
|
|
|
1752 #end if
|
|
|
1753
|
|
|
1754 #end if
|
|
|
1755
|
|
|
1756 #if str($CONDITIONAL_loop_cats.CONDITIONAL_SELECT_loop_cats) == "set":
|
|
|
1757 --loop-cats
|
|
|
1758
|
|
|
1759
|
|
|
1760 #if $str($CONDITIONAL_loop_cats.loop_cats_MOD_0_0):
|
|
|
1761 '${CONDITIONAL_loop_cats.loop_cats_MOD_0_0}'
|
|
|
1762 #end if
|
|
|
1763
|
|
|
1764 #end if
|
|
|
1765
|
|
|
1766 #if str($CONDITIONAL_no_id_header.CONDITIONAL_SELECT_no_id_header) == "set":
|
|
|
1767 --no-id-header
|
|
|
1768
|
|
|
1769
|
|
|
1770 #if $str($CONDITIONAL_no_id_header.no_id_header_MOD_0_0):
|
|
|
1771 '${CONDITIONAL_no_id_header.no_id_header_MOD_0_0}'
|
|
|
1772 #end if
|
|
|
1773
|
|
|
1774 #end if
|
|
|
1775
|
|
|
1776 #if str($CONDITIONAL_variance_standardize.CONDITIONAL_SELECT_variance_standardize) == "set":
|
|
|
1777 --variance-standardize
|
|
|
1778
|
|
|
1779
|
|
|
1780 #if $str($CONDITIONAL_variance_standardize.variance_standardize_MOD_0_0):
|
|
|
1781 '${CONDITIONAL_variance_standardize.variance_standardize_MOD_0_0}'
|
|
|
1782 #end if
|
|
|
1783
|
|
|
1784 #end if
|
|
|
1785
|
|
|
1786 #if str($CONDITIONAL_covar_variance_standardize.CONDITIONAL_SELECT_covar_variance_standardize) == "set":
|
|
|
1787 --covar-variance-standardize
|
|
|
1788
|
|
|
1789
|
|
|
1790 #if $str($CONDITIONAL_covar_variance_standardize.covar_variance_standardize_MOD_0_0):
|
|
|
1791 '${CONDITIONAL_covar_variance_standardize.covar_variance_standardize_MOD_0_0}'
|
|
|
1792 #end if
|
|
|
1793
|
|
|
1794 #end if
|
|
|
1795
|
|
|
1796 #if str($CONDITIONAL_quantile_normalize.CONDITIONAL_SELECT_quantile_normalize) == "set":
|
|
|
1797 --quantile-normalize
|
|
|
1798
|
|
|
1799
|
|
|
1800 #if $str($CONDITIONAL_quantile_normalize.quantile_normalize_MOD_0_0):
|
|
|
1801 '${CONDITIONAL_quantile_normalize.quantile_normalize_MOD_0_0}'
|
|
|
1802 #end if
|
|
|
1803
|
|
|
1804 #end if
|
|
|
1805
|
|
|
1806 #if str($CONDITIONAL_pheno_quantile_normalize.CONDITIONAL_SELECT_pheno_quantile_normalize) == "set":
|
|
|
1807 --pheno-quantile-normalize
|
|
|
1808
|
|
|
1809
|
|
|
1810 #if $str($CONDITIONAL_pheno_quantile_normalize.pheno_quantile_normalize_MOD_0_0):
|
|
|
1811 '${CONDITIONAL_pheno_quantile_normalize.pheno_quantile_normalize_MOD_0_0}'
|
|
|
1812 #end if
|
|
|
1813
|
|
|
1814 #end if
|
|
|
1815
|
|
|
1816 #if str($CONDITIONAL_covar_quantile_normalize.CONDITIONAL_SELECT_covar_quantile_normalize) == "set":
|
|
|
1817 --covar-quantile-normalize
|
|
|
1818
|
|
|
1819
|
|
|
1820 #if $str($CONDITIONAL_covar_quantile_normalize.covar_quantile_normalize_MOD_0_0):
|
|
|
1821 '${CONDITIONAL_covar_quantile_normalize.covar_quantile_normalize_MOD_0_0}'
|
|
|
1822 #end if
|
|
|
1823
|
|
|
1824 #end if
|
|
|
1825
|
|
|
1826 #if str($CONDITIONAL_chr.CONDITIONAL_SELECT_chr) == "set":
|
|
|
1827 --chr
|
|
|
1828
|
|
|
1829
|
|
|
1830 #if $str($CONDITIONAL_chr.chr_MOD_0_0):
|
|
|
1831 '${CONDITIONAL_chr.chr_MOD_0_0}'
|
|
|
1832 #end if
|
|
|
1833
|
|
|
1834 #end if
|
|
|
1835
|
|
|
1836 #if str($CONDITIONAL_not_chr.CONDITIONAL_SELECT_not_chr) == "set":
|
|
|
1837 --not-chr
|
|
|
1838
|
|
|
1839
|
|
|
1840 #if $str($CONDITIONAL_not_chr.not_chr_MOD_0_0):
|
|
|
1841 '${CONDITIONAL_not_chr.not_chr_MOD_0_0}'
|
|
|
1842 #end if
|
|
|
1843
|
|
|
1844 #end if
|
|
|
1845
|
|
|
1846 #if str($CONDITIONAL_autosome.CONDITIONAL_SELECT_autosome) == "set":
|
|
|
1847 --autosome
|
|
|
1848
|
|
|
1849
|
|
|
1850 #end if
|
|
|
1851
|
|
|
1852 #if str($CONDITIONAL_autosome_par.CONDITIONAL_SELECT_autosome_par) == "set":
|
|
|
1853 --autosome-par
|
|
|
1854
|
|
|
1855
|
|
|
1856 #end if
|
|
|
1857
|
|
|
1858 #if str($CONDITIONAL_snps_only.CONDITIONAL_SELECT_snps_only) == "set":
|
|
|
1859 --snps-only
|
|
|
1860
|
|
|
1861
|
|
|
1862 #if $str($CONDITIONAL_snps_only.snps_only_MOD_0_0):
|
|
|
1863 '${CONDITIONAL_snps_only.snps_only_MOD_0_0}'
|
|
|
1864 #end if
|
|
|
1865
|
|
|
1866 #end if
|
|
|
1867
|
|
|
1868 #if str($CONDITIONAL_from.CONDITIONAL_SELECT_from) == "set":
|
|
|
1869 --from
|
|
|
1870
|
|
|
1871
|
|
|
1872 #if $str($CONDITIONAL_from.from_MOD_0_0):
|
|
|
1873 '${CONDITIONAL_from.from_MOD_0_0}'
|
|
|
1874 #end if
|
|
|
1875
|
|
|
1876 #end if
|
|
|
1877
|
|
|
1878 #if str($CONDITIONAL_to.CONDITIONAL_SELECT_to) == "set":
|
|
|
1879 --to
|
|
|
1880
|
|
|
1881
|
|
|
1882 #if $str($CONDITIONAL_to.to_MOD_0_0):
|
|
|
1883 '${CONDITIONAL_to.to_MOD_0_0}'
|
|
|
1884 #end if
|
|
|
1885
|
|
|
1886 #end if
|
|
|
1887
|
|
|
1888 #if str($CONDITIONAL_snp.CONDITIONAL_SELECT_snp) == "set":
|
|
|
1889 --snp
|
|
|
1890
|
|
|
1891
|
|
|
1892 #if $str($CONDITIONAL_snp.snp_MOD_0_0):
|
|
|
1893 '${CONDITIONAL_snp.snp_MOD_0_0}'
|
|
|
1894 #end if
|
|
|
1895
|
|
|
1896 #end if
|
|
|
1897
|
|
|
1898 #if str($CONDITIONAL_exclude_snp.CONDITIONAL_SELECT_exclude_snp) == "set":
|
|
|
1899 --exclude-snp
|
|
|
1900
|
|
|
1901
|
|
|
1902 #if $str($CONDITIONAL_exclude_snp.exclude_snp_MOD_0_0):
|
|
|
1903 '${CONDITIONAL_exclude_snp.exclude_snp_MOD_0_0}'
|
|
|
1904 #end if
|
|
|
1905
|
|
|
1906 #end if
|
|
|
1907
|
|
|
1908 #if str($CONDITIONAL_window.CONDITIONAL_SELECT_window) == "set":
|
|
|
1909 --window
|
|
|
1910
|
|
|
1911
|
|
|
1912 #if $str($CONDITIONAL_window.window_MOD_0_0):
|
|
|
1913 '${CONDITIONAL_window.window_MOD_0_0}'
|
|
|
1914 #end if
|
|
|
1915
|
|
|
1916 #end if
|
|
|
1917
|
|
|
1918 #if str($CONDITIONAL_from_bp.CONDITIONAL_SELECT_from_bp) == "set":
|
|
|
1919 --from-bp
|
|
|
1920
|
|
|
1921
|
|
|
1922 #if $str($CONDITIONAL_from_bp.from_bp_MOD_0_0):
|
|
|
1923 '${CONDITIONAL_from_bp.from_bp_MOD_0_0}'
|
|
|
1924 #end if
|
|
|
1925
|
|
|
1926 #end if
|
|
|
1927
|
|
|
1928 #if str($CONDITIONAL_to_bp.CONDITIONAL_SELECT_to_bp) == "set":
|
|
|
1929 --to-bp
|
|
|
1930
|
|
|
1931
|
|
|
1932 #if $str($CONDITIONAL_to_bp.to_bp_MOD_0_0):
|
|
|
1933 '${CONDITIONAL_to_bp.to_bp_MOD_0_0}'
|
|
|
1934 #end if
|
|
|
1935
|
|
|
1936 #end if
|
|
|
1937
|
|
|
1938 #if str($CONDITIONAL_from_kb.CONDITIONAL_SELECT_from_kb) == "set":
|
|
|
1939 --from-kb
|
|
|
1940
|
|
|
1941
|
|
|
1942 #if $str($CONDITIONAL_from_kb.from_kb_MOD_0_0):
|
|
|
1943 '${CONDITIONAL_from_kb.from_kb_MOD_0_0}'
|
|
|
1944 #end if
|
|
|
1945
|
|
|
1946 #end if
|
|
|
1947
|
|
|
1948 #if str($CONDITIONAL_to_kb.CONDITIONAL_SELECT_to_kb) == "set":
|
|
|
1949 --to-kb
|
|
|
1950
|
|
|
1951
|
|
|
1952 #if $str($CONDITIONAL_to_kb.to_kb_MOD_0_0):
|
|
|
1953 '${CONDITIONAL_to_kb.to_kb_MOD_0_0}'
|
|
|
1954 #end if
|
|
|
1955
|
|
|
1956 #end if
|
|
|
1957
|
|
|
1958 #if str($CONDITIONAL_from_mb.CONDITIONAL_SELECT_from_mb) == "set":
|
|
|
1959 --from-mb
|
|
|
1960
|
|
|
1961
|
|
|
1962 #if $str($CONDITIONAL_from_mb.from_mb_MOD_0_0):
|
|
|
1963 '${CONDITIONAL_from_mb.from_mb_MOD_0_0}'
|
|
|
1964 #end if
|
|
|
1965
|
|
|
1966 #end if
|
|
|
1967
|
|
|
1968 #if str($CONDITIONAL_to_mb.CONDITIONAL_SELECT_to_mb) == "set":
|
|
|
1969 --to-mb
|
|
|
1970
|
|
|
1971
|
|
|
1972 #if $str($CONDITIONAL_to_mb.to_mb_MOD_0_0):
|
|
|
1973 '${CONDITIONAL_to_mb.to_mb_MOD_0_0}'
|
|
|
1974 #end if
|
|
|
1975
|
|
|
1976 #end if
|
|
|
1977
|
|
|
1978 #if str($CONDITIONAL_snps.CONDITIONAL_SELECT_snps) == "set":
|
|
|
1979 --snps
|
|
|
1980
|
|
|
1981
|
|
|
1982 #if $str($CONDITIONAL_snps.snps_MOD_0_0):
|
|
|
1983 '${CONDITIONAL_snps.snps_MOD_0_0}'
|
|
|
1984 #end if
|
|
|
1985
|
|
|
1986 #end if
|
|
|
1987
|
|
|
1988 #if str($CONDITIONAL_exclude_snps.CONDITIONAL_SELECT_exclude_snps) == "set":
|
|
|
1989 --exclude-snps
|
|
|
1990
|
|
|
1991
|
|
|
1992 #if $str($CONDITIONAL_exclude_snps.exclude_snps_MOD_0_0):
|
|
|
1993 '${CONDITIONAL_exclude_snps.exclude_snps_MOD_0_0}'
|
|
|
1994 #end if
|
|
|
1995
|
|
|
1996 #end if
|
|
|
1997
|
|
|
1998 #if str($CONDITIONAL_force_intersect.CONDITIONAL_SELECT_force_intersect) == "set":
|
|
|
1999 --force-intersect
|
|
|
2000
|
|
|
2001
|
|
|
2002 #end if
|
|
|
2003
|
|
|
2004 #if str($CONDITIONAL_thin.CONDITIONAL_SELECT_thin) == "set":
|
|
|
2005 --thin
|
|
|
2006
|
|
|
2007
|
|
|
2008 #if $str($CONDITIONAL_thin.thin_MOD_0_0):
|
|
|
2009 '${CONDITIONAL_thin.thin_MOD_0_0}'
|
|
|
2010 #end if
|
|
|
2011
|
|
|
2012 #end if
|
|
|
2013
|
|
|
2014 #if str($CONDITIONAL_thin_count.CONDITIONAL_SELECT_thin_count) == "set":
|
|
|
2015 --thin-count
|
|
|
2016
|
|
|
2017
|
|
|
2018 #if $str($CONDITIONAL_thin_count.thin_count_MOD_0_0):
|
|
|
2019 '${CONDITIONAL_thin_count.thin_count_MOD_0_0}'
|
|
|
2020 #end if
|
|
|
2021
|
|
|
2022 #end if
|
|
|
2023
|
|
|
2024 #if str($CONDITIONAL_bp_space.CONDITIONAL_SELECT_bp_space) == "set":
|
|
|
2025 --bp-space
|
|
|
2026
|
|
|
2027
|
|
|
2028 #if $str($CONDITIONAL_bp_space.bp_space_MOD_0_0):
|
|
|
2029 '${CONDITIONAL_bp_space.bp_space_MOD_0_0}'
|
|
|
2030 #end if
|
|
|
2031
|
|
|
2032 #end if
|
|
|
2033
|
|
|
2034 #if str($CONDITIONAL_thin_indiv.CONDITIONAL_SELECT_thin_indiv) == "set":
|
|
|
2035 --thin-indiv
|
|
|
2036
|
|
|
2037
|
|
|
2038 #if $str($CONDITIONAL_thin_indiv.thin_indiv_MOD_0_0):
|
|
|
2039 '${CONDITIONAL_thin_indiv.thin_indiv_MOD_0_0}'
|
|
|
2040 #end if
|
|
|
2041
|
|
|
2042 #end if
|
|
|
2043
|
|
|
2044 #if str($CONDITIONAL_thin_indiv_count.CONDITIONAL_SELECT_thin_indiv_count) == "set":
|
|
|
2045 --thin-indiv-count
|
|
|
2046
|
|
|
2047
|
|
|
2048 #if $str($CONDITIONAL_thin_indiv_count.thin_indiv_count_MOD_0_0):
|
|
|
2049 '${CONDITIONAL_thin_indiv_count.thin_indiv_count_MOD_0_0}'
|
|
|
2050 #end if
|
|
|
2051
|
|
|
2052 #end if
|
|
|
2053
|
|
|
2054 #if str($CONDITIONAL_keep_col_match.CONDITIONAL_SELECT_keep_col_match) == "set":
|
|
|
2055 --keep-col-match
|
|
|
2056
|
|
|
2057
|
|
|
2058 #if $CONDITIONAL_keep_col_match.keep_col_match_MOD_0_0:
|
|
|
2059 '${CONDITIONAL_keep_col_match.keep_col_match_MOD_0_0}'
|
|
|
2060 #end if
|
|
|
2061
|
|
|
2062 #if $str($CONDITIONAL_keep_col_match.keep_col_match_MOD_1_0):
|
|
|
2063 '${CONDITIONAL_keep_col_match.keep_col_match_MOD_1_0}'
|
|
|
2064 #end if
|
|
|
2065
|
|
|
2066 #end if
|
|
|
2067
|
|
|
2068 #if str($CONDITIONAL_keep_col_match_name.CONDITIONAL_SELECT_keep_col_match_name) == "set":
|
|
|
2069 --keep-col-match-name
|
|
|
2070
|
|
|
2071
|
|
|
2072 #if $str($CONDITIONAL_keep_col_match_name.keep_col_match_name_MOD_0_0):
|
|
|
2073 '${CONDITIONAL_keep_col_match_name.keep_col_match_name_MOD_0_0}'
|
|
|
2074 #end if
|
|
|
2075
|
|
|
2076 #end if
|
|
|
2077
|
|
|
2078 #if str($CONDITIONAL_keep_col_match_num.CONDITIONAL_SELECT_keep_col_match_num) == "set":
|
|
|
2079 --keep-col-match-num
|
|
|
2080
|
|
|
2081
|
|
|
2082 #if $str($CONDITIONAL_keep_col_match_num.keep_col_match_num_MOD_0_0):
|
|
|
2083 '${CONDITIONAL_keep_col_match_num.keep_col_match_num_MOD_0_0}'
|
|
|
2084 #end if
|
|
|
2085
|
|
|
2086 #end if
|
|
|
2087
|
|
|
2088 #if str($CONDITIONAL_geno.CONDITIONAL_SELECT_geno) == "set":
|
|
|
2089 --geno
|
|
|
2090
|
|
|
2091
|
|
|
2092 #if $str($CONDITIONAL_geno.geno_MOD_0_0):
|
|
|
2093 '${CONDITIONAL_geno.geno_MOD_0_0}'
|
|
|
2094 #end if
|
|
|
2095
|
|
|
2096 #if $str($CONDITIONAL_geno.CONDITIONAL_geno_MOD_1.CONDITIONAL_SELECT_geno_MOD_1) == 'from_list'
|
|
|
2097 '${CONDITIONAL_geno.CONDITIONAL_geno_MOD_1.geno_MOD_1}'
|
|
|
2098 #end if
|
|
|
2099
|
|
|
2100
|
|
|
2101 #end if
|
|
|
2102
|
|
|
2103 #if str($CONDITIONAL_mind.CONDITIONAL_SELECT_mind) == "set":
|
|
|
2104 --mind
|
|
|
2105
|
|
|
2106
|
|
|
2107 #if $str($CONDITIONAL_mind.mind_MOD_0_0):
|
|
|
2108 '${CONDITIONAL_mind.mind_MOD_0_0}'
|
|
|
2109 #end if
|
|
|
2110
|
|
|
2111 #if $str($CONDITIONAL_mind.CONDITIONAL_mind_MOD_1.CONDITIONAL_SELECT_mind_MOD_1) == 'from_list'
|
|
|
2112 '${CONDITIONAL_mind.CONDITIONAL_mind_MOD_1.mind_MOD_1}'
|
|
|
2113 #end if
|
|
|
2114
|
|
|
2115
|
|
|
2116 #end if
|
|
|
2117
|
|
|
2118 #if str($CONDITIONAL_require_pheno.CONDITIONAL_SELECT_require_pheno) == "set":
|
|
|
2119 --require-pheno
|
|
|
2120
|
|
|
2121
|
|
|
2122 #if $str($CONDITIONAL_require_pheno.require_pheno_MOD_0_0):
|
|
|
2123 '${CONDITIONAL_require_pheno.require_pheno_MOD_0_0}'
|
|
|
2124 #end if
|
|
|
2125
|
|
|
2126 #end if
|
|
|
2127
|
|
|
2128 #if str($CONDITIONAL_require_covar.CONDITIONAL_SELECT_require_covar) == "set":
|
|
|
2129 --require-covar
|
|
|
2130
|
|
|
2131
|
|
|
2132 #if $str($CONDITIONAL_require_covar.require_covar_MOD_0_0):
|
|
|
2133 '${CONDITIONAL_require_covar.require_covar_MOD_0_0}'
|
|
|
2134 #end if
|
|
|
2135
|
|
|
2136 #end if
|
|
|
2137
|
|
|
2138 #if str($CONDITIONAL_maf.CONDITIONAL_SELECT_maf) == "set":
|
|
|
2139 --maf
|
|
|
2140
|
|
|
2141
|
|
|
2142 #if $str($CONDITIONAL_maf.maf_MOD_0_0):
|
|
|
2143 '${CONDITIONAL_maf.maf_MOD_0_0}'
|
|
|
2144 #end if
|
|
|
2145
|
|
|
2146 #if $str($CONDITIONAL_maf.maf_MOD_1_0):
|
|
|
2147 '${CONDITIONAL_maf.maf_MOD_1_0}'
|
|
|
2148 #end if
|
|
|
2149
|
|
|
2150 #end if
|
|
|
2151
|
|
|
2152 #if str($CONDITIONAL_max_maf.CONDITIONAL_SELECT_max_maf) == "set":
|
|
|
2153 --max-maf
|
|
|
2154
|
|
|
2155
|
|
|
2156 #if $str($CONDITIONAL_max_maf.max_maf_MOD_0_0):
|
|
|
2157 '${CONDITIONAL_max_maf.max_maf_MOD_0_0}'
|
|
|
2158 #end if
|
|
|
2159
|
|
|
2160 #if $str($CONDITIONAL_max_maf.max_maf_MOD_1_0):
|
|
|
2161 '${CONDITIONAL_max_maf.max_maf_MOD_1_0}'
|
|
|
2162 #end if
|
|
|
2163
|
|
|
2164 #end if
|
|
|
2165
|
|
|
2166 #if str($CONDITIONAL_mac.CONDITIONAL_SELECT_mac) == "set":
|
|
|
2167 --mac
|
|
|
2168
|
|
|
2169
|
|
|
2170 #if $str($CONDITIONAL_mac.mac_MOD_0_0):
|
|
|
2171 '${CONDITIONAL_mac.mac_MOD_0_0}'
|
|
|
2172 #end if
|
|
|
2173
|
|
|
2174 #if $str($CONDITIONAL_mac.mac_MOD_1_0):
|
|
|
2175 '${CONDITIONAL_mac.mac_MOD_1_0}'
|
|
|
2176 #end if
|
|
|
2177
|
|
|
2178 #end if
|
|
|
2179
|
|
|
2180 #if str($CONDITIONAL_max_mac.CONDITIONAL_SELECT_max_mac) == "set":
|
|
|
2181 --max-mac
|
|
|
2182
|
|
|
2183
|
|
|
2184 #if $str($CONDITIONAL_max_mac.max_mac_MOD_0_0):
|
|
|
2185 '${CONDITIONAL_max_mac.max_mac_MOD_0_0}'
|
|
|
2186 #end if
|
|
|
2187
|
|
|
2188 #if $str($CONDITIONAL_max_mac.max_mac_MOD_1_0):
|
|
|
2189 '${CONDITIONAL_max_mac.max_mac_MOD_1_0}'
|
|
|
2190 #end if
|
|
|
2191
|
|
|
2192 #end if
|
|
|
2193
|
|
|
2194 #if str($CONDITIONAL_maf_succ.CONDITIONAL_SELECT_maf_succ) == "set":
|
|
|
2195 --maf-succ
|
|
|
2196
|
|
|
2197
|
|
|
2198 #end if
|
|
|
2199
|
|
|
2200 #if str($CONDITIONAL_min_alleles.CONDITIONAL_SELECT_min_alleles) == "set":
|
|
|
2201 --min-alleles
|
|
|
2202
|
|
|
2203
|
|
|
2204 #if $str($CONDITIONAL_min_alleles.min_alleles_MOD_0_0):
|
|
|
2205 '${CONDITIONAL_min_alleles.min_alleles_MOD_0_0}'
|
|
|
2206 #end if
|
|
|
2207
|
|
|
2208 #end if
|
|
|
2209
|
|
|
2210 #if str($CONDITIONAL_max_alleles.CONDITIONAL_SELECT_max_alleles) == "set":
|
|
|
2211 --max-alleles
|
|
|
2212
|
|
|
2213
|
|
|
2214 #if $str($CONDITIONAL_max_alleles.max_alleles_MOD_0_0):
|
|
|
2215 '${CONDITIONAL_max_alleles.max_alleles_MOD_0_0}'
|
|
|
2216 #end if
|
|
|
2217
|
|
|
2218 #end if
|
|
|
2219
|
|
|
2220 #if str($CONDITIONAL_read_freq.CONDITIONAL_SELECT_read_freq) == "set":
|
|
|
2221 --read-freq
|
|
|
2222
|
|
|
2223
|
|
|
2224 #if $str($CONDITIONAL_read_freq.read_freq_MOD_0_0):
|
|
|
2225 '${CONDITIONAL_read_freq.read_freq_MOD_0_0}'
|
|
|
2226 #end if
|
|
|
2227
|
|
|
2228 #end if
|
|
|
2229
|
|
|
2230 #if str($CONDITIONAL_hwe.CONDITIONAL_SELECT_hwe) == "set":
|
|
|
2231 --hwe
|
|
|
2232
|
|
|
2233
|
|
|
2234 #if $str($CONDITIONAL_hwe.hwe_MOD_0_0):
|
|
|
2235 '${CONDITIONAL_hwe.hwe_MOD_0_0}'
|
|
|
2236 #end if
|
|
|
2237
|
|
|
2238 #if $str($CONDITIONAL_hwe.hwe_MOD_1_0):
|
|
|
2239 '${CONDITIONAL_hwe.hwe_MOD_1_0}'
|
|
|
2240 #end if
|
|
|
2241
|
|
|
2242 #if $str($CONDITIONAL_hwe.hwe_MOD_2_0):
|
|
|
2243 '${CONDITIONAL_hwe.hwe_MOD_2_0}'
|
|
|
2244 #end if
|
|
|
2245
|
|
|
2246 #end if
|
|
|
2247
|
|
|
2248 #if str($CONDITIONAL_mach_r2_filter.CONDITIONAL_SELECT_mach_r2_filter) == "set":
|
|
|
2249 --mach-r2-filter
|
|
|
2250
|
|
|
2251
|
|
|
2252 #if $str($CONDITIONAL_mach_r2_filter.mach_r2_filter_MOD_0_0):
|
|
|
2253 '${CONDITIONAL_mach_r2_filter.mach_r2_filter_MOD_0_0}'
|
|
|
2254 #end if
|
|
|
2255
|
|
|
2256 #if $str($CONDITIONAL_mach_r2_filter.mach_r2_filter_MOD_1_0):
|
|
|
2257 '${CONDITIONAL_mach_r2_filter.mach_r2_filter_MOD_1_0}'
|
|
|
2258 #end if
|
|
|
2259
|
|
|
2260 #end if
|
|
|
2261
|
|
|
2262 #if str($CONDITIONAL_minimac3_r2_filter.CONDITIONAL_SELECT_minimac3_r2_filter) == "set":
|
|
|
2263 --minimac3-r2-filter
|
|
|
2264
|
|
|
2265
|
|
|
2266 #if $str($CONDITIONAL_minimac3_r2_filter.minimac3_r2_filter_MOD_0_0):
|
|
|
2267 '${CONDITIONAL_minimac3_r2_filter.minimac3_r2_filter_MOD_0_0}'
|
|
|
2268 #end if
|
|
|
2269
|
|
|
2270 #if $str($CONDITIONAL_minimac3_r2_filter.minimac3_r2_filter_MOD_1_0):
|
|
|
2271 '${CONDITIONAL_minimac3_r2_filter.minimac3_r2_filter_MOD_1_0}'
|
|
|
2272 #end if
|
|
|
2273
|
|
|
2274 #end if
|
|
|
2275
|
|
|
2276 #if str($CONDITIONAL_keep_females.CONDITIONAL_SELECT_keep_females) == "set":
|
|
|
2277 --keep-females
|
|
|
2278
|
|
|
2279
|
|
|
2280 #end if
|
|
|
2281
|
|
|
2282 #if str($CONDITIONAL_keep_males.CONDITIONAL_SELECT_keep_males) == "set":
|
|
|
2283 --keep-males
|
|
|
2284
|
|
|
2285
|
|
|
2286 #end if
|
|
|
2287
|
|
|
2288 #if str($CONDITIONAL_keep_nosex.CONDITIONAL_SELECT_keep_nosex) == "set":
|
|
|
2289 --keep-nosex
|
|
|
2290
|
|
|
2291
|
|
|
2292 #end if
|
|
|
2293
|
|
|
2294 #if str($CONDITIONAL_remove_females.CONDITIONAL_SELECT_remove_females) == "set":
|
|
|
2295 --remove-females
|
|
|
2296
|
|
|
2297
|
|
|
2298 #end if
|
|
|
2299
|
|
|
2300 #if str($CONDITIONAL_remove_males.CONDITIONAL_SELECT_remove_males) == "set":
|
|
|
2301 --remove-males
|
|
|
2302
|
|
|
2303
|
|
|
2304 #end if
|
|
|
2305
|
|
|
2306 #if str($CONDITIONAL_remove_nosex.CONDITIONAL_SELECT_remove_nosex) == "set":
|
|
|
2307 --remove-nosex
|
|
|
2308
|
|
|
2309
|
|
|
2310 #end if
|
|
|
2311
|
|
|
2312 #if str($CONDITIONAL_keep_founders.CONDITIONAL_SELECT_keep_founders) == "set":
|
|
|
2313 --keep-founders
|
|
|
2314
|
|
|
2315
|
|
|
2316 #end if
|
|
|
2317
|
|
|
2318 #if str($CONDITIONAL_keep_nonfounders.CONDITIONAL_SELECT_keep_nonfounders) == "set":
|
|
|
2319 --keep-nonfounders
|
|
|
2320
|
|
|
2321
|
|
|
2322 #end if
|
|
|
2323
|
|
|
2324 #if str($CONDITIONAL_keep_if.CONDITIONAL_SELECT_keep_if) == "set":
|
|
|
2325 --keep-if
|
|
|
2326
|
|
|
2327
|
|
|
2328 #if $str($CONDITIONAL_keep_if.keep_if_MOD_0_0):
|
|
|
2329 '${CONDITIONAL_keep_if.keep_if_MOD_0_0}'
|
|
|
2330 #end if
|
|
|
2331
|
|
|
2332 #if $str($CONDITIONAL_keep_if.keep_if_MOD_1_0):
|
|
|
2333 '${CONDITIONAL_keep_if.keep_if_MOD_1_0}'
|
|
|
2334 #end if
|
|
|
2335
|
|
|
2336 #if $str($CONDITIONAL_keep_if.keep_if_MOD_2_0):
|
|
|
2337 '${CONDITIONAL_keep_if.keep_if_MOD_2_0}'
|
|
|
2338 #end if
|
|
|
2339
|
|
|
2340 #end if
|
|
|
2341
|
|
|
2342 #if str($CONDITIONAL_remove_if.CONDITIONAL_SELECT_remove_if) == "set":
|
|
|
2343 --remove-if
|
|
|
2344
|
|
|
2345
|
|
|
2346 #if $str($CONDITIONAL_remove_if.remove_if_MOD_0_0):
|
|
|
2347 '${CONDITIONAL_remove_if.remove_if_MOD_0_0}'
|
|
|
2348 #end if
|
|
|
2349
|
|
|
2350 #if $str($CONDITIONAL_remove_if.remove_if_MOD_1_0):
|
|
|
2351 '${CONDITIONAL_remove_if.remove_if_MOD_1_0}'
|
|
|
2352 #end if
|
|
|
2353
|
|
|
2354 #if $str($CONDITIONAL_remove_if.remove_if_MOD_2_0):
|
|
|
2355 '${CONDITIONAL_remove_if.remove_if_MOD_2_0}'
|
|
|
2356 #end if
|
|
|
2357
|
|
|
2358 #end if
|
|
|
2359
|
|
|
2360 #if str($CONDITIONAL_nonfounders.CONDITIONAL_SELECT_nonfounders) == "set":
|
|
|
2361 --nonfounders
|
|
|
2362
|
|
|
2363
|
|
|
2364 #end if
|
|
|
2365
|
|
|
2366 #if str($CONDITIONAL_bad_freqs.CONDITIONAL_SELECT_bad_freqs) == "set":
|
|
|
2367 --bad-freqs
|
|
|
2368
|
|
|
2369
|
|
|
2370 #end if
|
|
|
2371
|
|
|
2372 #if str($CONDITIONAL_export_allele.CONDITIONAL_SELECT_export_allele) == "set":
|
|
|
2373 --export-allele
|
|
|
2374
|
|
|
2375
|
|
|
2376 #if $str($CONDITIONAL_export_allele.export_allele_MOD_0_0):
|
|
|
2377 '${CONDITIONAL_export_allele.export_allele_MOD_0_0}'
|
|
|
2378 #end if
|
|
|
2379
|
|
|
2380 #end if
|
|
|
2381
|
|
|
2382 #if str($CONDITIONAL_output_chr.CONDITIONAL_SELECT_output_chr) == "set":
|
|
|
2383 --output-chr
|
|
|
2384
|
|
|
2385
|
|
|
2386 #if $str($CONDITIONAL_output_chr.output_chr_MOD_0_0):
|
|
|
2387 '${CONDITIONAL_output_chr.output_chr_MOD_0_0}'
|
|
|
2388 #end if
|
|
|
2389
|
|
|
2390 #end if
|
|
|
2391
|
|
|
2392 #if str($CONDITIONAL_output_missing_genotype.CONDITIONAL_SELECT_output_missing_genotype) == "set":
|
|
|
2393 --output-missing-genotype
|
|
|
2394
|
|
|
2395
|
|
|
2396 #if $str($CONDITIONAL_output_missing_genotype.output_missing_genotype_MOD_0_0):
|
|
|
2397 '${CONDITIONAL_output_missing_genotype.output_missing_genotype_MOD_0_0}'
|
|
|
2398 #end if
|
|
|
2399
|
|
|
2400 #end if
|
|
|
2401
|
|
|
2402 #if str($CONDITIONAL_output_missing_phenotype.CONDITIONAL_SELECT_output_missing_phenotype) == "set":
|
|
|
2403 --output-missing-phenotype
|
|
|
2404
|
|
|
2405
|
|
|
2406 #if $str($CONDITIONAL_output_missing_phenotype.output_missing_phenotype_MOD_0_0):
|
|
|
2407 '${CONDITIONAL_output_missing_phenotype.output_missing_phenotype_MOD_0_0}'
|
|
|
2408 #end if
|
|
|
2409
|
|
|
2410 #end if
|
|
|
2411
|
|
|
2412 #if str($CONDITIONAL_sort_vars.CONDITIONAL_SELECT_sort_vars) == "set":
|
|
|
2413 --sort-vars
|
|
|
2414
|
|
|
2415
|
|
|
2416 #if $str($CONDITIONAL_sort_vars.sort_vars_MOD_0_0):
|
|
|
2417 '${CONDITIONAL_sort_vars.sort_vars_MOD_0_0}'
|
|
|
2418 #end if
|
|
|
2419
|
|
|
2420 #end if
|
|
|
2421
|
|
|
2422 #if str($CONDITIONAL_set_hh_missing.CONDITIONAL_SELECT_set_hh_missing) == "set":
|
|
|
2423 --set-hh-missing
|
|
|
2424
|
|
|
2425
|
|
|
2426 #if $str($CONDITIONAL_set_hh_missing.set_hh_missing_MOD_0_0):
|
|
|
2427 '${CONDITIONAL_set_hh_missing.set_hh_missing_MOD_0_0}'
|
|
|
2428 #end if
|
|
|
2429
|
|
|
2430 #end if
|
|
|
2431
|
|
|
2432 #if str($CONDITIONAL_set_mixed_mt_missing.CONDITIONAL_SELECT_set_mixed_mt_missing) == "set":
|
|
|
2433 --set-mixed-mt-missing
|
|
|
2434
|
|
|
2435
|
|
|
2436 #if $str($CONDITIONAL_set_mixed_mt_missing.set_mixed_mt_missing_MOD_0_0):
|
|
|
2437 '${CONDITIONAL_set_mixed_mt_missing.set_mixed_mt_missing_MOD_0_0}'
|
|
|
2438 #end if
|
|
|
2439
|
|
|
2440 #end if
|
|
|
2441
|
|
|
2442 #if str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_OVERLOADED_SELECT_split_par) == "form_0":
|
|
|
2443 #if str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.CONDITIONAL_SELECT_split_par) == "set":
|
|
|
2444 --split-par
|
|
|
2445
|
|
|
2446 #if $str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_0_0):
|
|
|
2447 '${CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_0_0}'
|
|
|
2448 #end if
|
|
|
2449 #if $str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_1_0):
|
|
|
2450 '${CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_1_0}'
|
|
|
2451 #end if
|
|
|
2452 #end if
|
|
|
2453 #end if
|
|
|
2454
|
|
|
2455 #if str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_OVERLOADED_SELECT_split_par) == "form_1":
|
|
|
2456 #if str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.CONDITIONAL_SELECT_split_par) == "set":
|
|
|
2457 --split-par
|
|
|
2458
|
|
|
2459 #if $str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_0_0):
|
|
|
2460 '${CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_0_0}'
|
|
|
2461 #end if
|
|
|
2462 #if $str($CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_1_0):
|
|
|
2463 '${CONDITIONAL_OVERLOADED_split_par.CONDITIONAL_split_par.split_par_MOD_1_0}'
|
|
|
2464 #end if
|
|
|
2465 #end if
|
|
|
2466 #end if
|
|
|
2467
|
|
|
2468 #if str($CONDITIONAL_merge_par.CONDITIONAL_SELECT_merge_par) == "set":
|
|
|
2469 --merge-par
|
|
|
2470
|
|
|
2471
|
|
|
2472 #end if
|
|
|
2473
|
|
|
2474 #if str($CONDITIONAL_merge_x.CONDITIONAL_SELECT_merge_x) == "set":
|
|
|
2475 --merge-x
|
|
|
2476
|
|
|
2477
|
|
|
2478 #end if
|
|
|
2479
|
|
|
2480 #if str($CONDITIONAL_set_missing_var_ids.CONDITIONAL_SELECT_set_missing_var_ids) == "set":
|
|
|
2481 --set-missing-var-ids
|
|
|
2482
|
|
|
2483
|
|
|
2484 #if $str($CONDITIONAL_set_missing_var_ids.set_missing_var_ids_MOD_0_0):
|
|
|
2485 '${CONDITIONAL_set_missing_var_ids.set_missing_var_ids_MOD_0_0}'
|
|
|
2486 #end if
|
|
|
2487
|
|
|
2488 #end if
|
|
|
2489
|
|
|
2490 #if str($CONDITIONAL_set_all_var_ids.CONDITIONAL_SELECT_set_all_var_ids) == "set":
|
|
|
2491 --set-all-var-ids
|
|
|
2492
|
|
|
2493
|
|
|
2494 #if $str($CONDITIONAL_set_all_var_ids.set_all_var_ids_MOD_0_0):
|
|
|
2495 '${CONDITIONAL_set_all_var_ids.set_all_var_ids_MOD_0_0}'
|
|
|
2496 #end if
|
|
|
2497
|
|
|
2498 #end if
|
|
|
2499
|
|
|
2500 #if str($CONDITIONAL_var_id_multi.CONDITIONAL_SELECT_var_id_multi) == "set":
|
|
|
2501 --var-id-multi
|
|
|
2502
|
|
|
2503
|
|
|
2504 #if $str($CONDITIONAL_var_id_multi.var_id_multi_MOD_0_0):
|
|
|
2505 '${CONDITIONAL_var_id_multi.var_id_multi_MOD_0_0}'
|
|
|
2506 #end if
|
|
|
2507
|
|
|
2508 #end if
|
|
|
2509
|
|
|
2510 #if str($CONDITIONAL_var_id_multi_nonsnp.CONDITIONAL_SELECT_var_id_multi_nonsnp) == "set":
|
|
|
2511 --var-id-multi-nonsnp
|
|
|
2512
|
|
|
2513
|
|
|
2514 #if $str($CONDITIONAL_var_id_multi_nonsnp.var_id_multi_nonsnp_MOD_0_0):
|
|
|
2515 '${CONDITIONAL_var_id_multi_nonsnp.var_id_multi_nonsnp_MOD_0_0}'
|
|
|
2516 #end if
|
|
|
2517
|
|
|
2518 #end if
|
|
|
2519
|
|
|
2520 #if str($CONDITIONAL_new_id_max_allele_len.CONDITIONAL_SELECT_new_id_max_allele_len) == "set":
|
|
|
2521 --new-id-max-allele-len
|
|
|
2522
|
|
|
2523
|
|
|
2524 #if $str($CONDITIONAL_new_id_max_allele_len.new_id_max_allele_len_MOD_0_0):
|
|
|
2525 '${CONDITIONAL_new_id_max_allele_len.new_id_max_allele_len_MOD_0_0}'
|
|
|
2526 #end if
|
|
|
2527
|
|
|
2528 #if $str($CONDITIONAL_new_id_max_allele_len.CONDITIONAL_new_id_max_allele_len_MOD_1.CONDITIONAL_SELECT_new_id_max_allele_len_MOD_1) == 'from_list'
|
|
|
2529 '${CONDITIONAL_new_id_max_allele_len.CONDITIONAL_new_id_max_allele_len_MOD_1.new_id_max_allele_len_MOD_1}'
|
|
|
2530 #end if
|
|
|
2531
|
|
|
2532
|
|
|
2533 #end if
|
|
|
2534
|
|
|
2535 #if str($CONDITIONAL_missing_var_code.CONDITIONAL_SELECT_missing_var_code) == "set":
|
|
|
2536 --missing-var-code
|
|
|
2537
|
|
|
2538
|
|
|
2539 #if $str($CONDITIONAL_missing_var_code.missing_var_code_MOD_0_0):
|
|
|
2540 '${CONDITIONAL_missing_var_code.missing_var_code_MOD_0_0}'
|
|
|
2541 #end if
|
|
|
2542
|
|
|
2543 #end if
|
|
|
2544
|
|
|
2545 #if str($CONDITIONAL_update_map.CONDITIONAL_SELECT_update_map) == "set":
|
|
|
2546 --update-map
|
|
|
2547
|
|
|
2548
|
|
|
2549 #if $CONDITIONAL_update_map.update_map_MOD_0_0:
|
|
|
2550 '${CONDITIONAL_update_map.update_map_MOD_0_0}'
|
|
|
2551 #end if
|
|
|
2552
|
|
|
2553 #if $str($CONDITIONAL_update_map.update_map_MOD_1_0):
|
|
|
2554 '${CONDITIONAL_update_map.update_map_MOD_1_0}'
|
|
|
2555 #end if
|
|
|
2556
|
|
|
2557 #if $str($CONDITIONAL_update_map.update_map_MOD_2_0):
|
|
|
2558 '${CONDITIONAL_update_map.update_map_MOD_2_0}'
|
|
|
2559 #end if
|
|
|
2560
|
|
|
2561 #if $str($CONDITIONAL_update_map.update_map_MOD_3_0):
|
|
|
2562 '${CONDITIONAL_update_map.update_map_MOD_3_0}'
|
|
|
2563 #end if
|
|
|
2564
|
|
|
2565 #end if
|
|
|
2566
|
|
|
2567 #if str($CONDITIONAL_update_name.CONDITIONAL_SELECT_update_name) == "set":
|
|
|
2568 --update-name
|
|
|
2569
|
|
|
2570
|
|
|
2571 #if $CONDITIONAL_update_name.update_name_MOD_0_0:
|
|
|
2572 '${CONDITIONAL_update_name.update_name_MOD_0_0}'
|
|
|
2573 #end if
|
|
|
2574
|
|
|
2575 #if $str($CONDITIONAL_update_name.update_name_MOD_1_0):
|
|
|
2576 '${CONDITIONAL_update_name.update_name_MOD_1_0}'
|
|
|
2577 #end if
|
|
|
2578
|
|
|
2579 #if $str($CONDITIONAL_update_name.update_name_MOD_2_0):
|
|
|
2580 '${CONDITIONAL_update_name.update_name_MOD_2_0}'
|
|
|
2581 #end if
|
|
|
2582
|
|
|
2583 #if $str($CONDITIONAL_update_name.update_name_MOD_3_0):
|
|
|
2584 '${CONDITIONAL_update_name.update_name_MOD_3_0}'
|
|
|
2585 #end if
|
|
|
2586
|
|
|
2587 #end if
|
|
|
2588
|
|
|
2589 #if str($CONDITIONAL_recover_var_ids.CONDITIONAL_SELECT_recover_var_ids) == "set":
|
|
|
2590 --recover-var-ids
|
|
|
2591
|
|
|
2592
|
|
|
2593 #if $str($CONDITIONAL_recover_var_ids.recover_var_ids_MOD_0_0):
|
|
|
2594 '${CONDITIONAL_recover_var_ids.recover_var_ids_MOD_0_0}'
|
|
|
2595 #end if
|
|
|
2596
|
|
|
2597 #if $str($CONDITIONAL_recover_var_ids.recover_var_ids_MOD_1_0):
|
|
|
2598 '${CONDITIONAL_recover_var_ids.recover_var_ids_MOD_1_0}'
|
|
|
2599 #end if
|
|
|
2600
|
|
|
2601 #if $str($CONDITIONAL_recover_var_ids.CONDITIONAL_recover_var_ids_MOD_2.CONDITIONAL_SELECT_recover_var_ids_MOD_2) == 'from_list'
|
|
|
2602 '${CONDITIONAL_recover_var_ids.CONDITIONAL_recover_var_ids_MOD_2.recover_var_ids_MOD_2}'
|
|
|
2603 #end if
|
|
|
2604
|
|
|
2605
|
|
|
2606 #if $str($CONDITIONAL_recover_var_ids.recover_var_ids_MOD_3_0):
|
|
|
2607 '${CONDITIONAL_recover_var_ids.recover_var_ids_MOD_3_0}'
|
|
|
2608 #end if
|
|
|
2609
|
|
|
2610 #end if
|
|
|
2611
|
|
|
2612 #if str($CONDITIONAL_update_alleles.CONDITIONAL_SELECT_update_alleles) == "set":
|
|
|
2613 --update-alleles
|
|
|
2614
|
|
|
2615
|
|
|
2616 #if $CONDITIONAL_update_alleles.update_alleles_MOD_0_0:
|
|
|
2617 '${CONDITIONAL_update_alleles.update_alleles_MOD_0_0}'
|
|
|
2618 #end if
|
|
|
2619
|
|
|
2620 #end if
|
|
|
2621
|
|
|
2622 #if str($CONDITIONAL_update_ids.CONDITIONAL_SELECT_update_ids) == "set":
|
|
|
2623 --update-ids
|
|
|
2624
|
|
|
2625
|
|
|
2626 #if $CONDITIONAL_update_ids.update_ids_MOD_0_0:
|
|
|
2627 '${CONDITIONAL_update_ids.update_ids_MOD_0_0}'
|
|
|
2628 #end if
|
|
|
2629
|
|
|
2630 #end if
|
|
|
2631
|
|
|
2632 #if str($CONDITIONAL_update_parents.CONDITIONAL_SELECT_update_parents) == "set":
|
|
|
2633 --update-parents
|
|
|
2634
|
|
|
2635
|
|
|
2636 #if $CONDITIONAL_update_parents.update_parents_MOD_0_0:
|
|
|
2637 '${CONDITIONAL_update_parents.update_parents_MOD_0_0}'
|
|
|
2638 #end if
|
|
|
2639
|
|
|
2640 #end if
|
|
|
2641
|
|
|
2642 #if str($CONDITIONAL_update_sex.CONDITIONAL_SELECT_update_sex) == "set":
|
|
|
2643 --update-sex
|
|
|
2644
|
|
|
2645
|
|
|
2646 #if $CONDITIONAL_update_sex.update_sex_MOD_0_0:
|
|
|
2647 '${CONDITIONAL_update_sex.update_sex_MOD_0_0}'
|
|
|
2648 #end if
|
|
|
2649
|
|
|
2650 #if $str($CONDITIONAL_update_sex.update_sex_MOD_1_0):
|
|
|
2651 '${CONDITIONAL_update_sex.update_sex_MOD_1_0}'
|
|
|
2652 #end if
|
|
|
2653
|
|
|
2654 #if $str($CONDITIONAL_update_sex.update_sex_MOD_2_0):
|
|
|
2655 '${CONDITIONAL_update_sex.update_sex_MOD_2_0}'
|
|
|
2656 #end if
|
|
|
2657
|
|
|
2658 #end if
|
|
|
2659
|
|
|
2660 #if str($CONDITIONAL_real_ref_alleles.CONDITIONAL_SELECT_real_ref_alleles) == "set":
|
|
|
2661 --real-ref-alleles
|
|
|
2662
|
|
|
2663
|
|
|
2664 #end if
|
|
|
2665
|
|
|
2666 #if str($CONDITIONAL_maj_ref.CONDITIONAL_SELECT_maj_ref) == "set":
|
|
|
2667 --maj-ref
|
|
|
2668
|
|
|
2669
|
|
|
2670 #if $str($CONDITIONAL_maj_ref.maj_ref_MOD_0_0):
|
|
|
2671 '${CONDITIONAL_maj_ref.maj_ref_MOD_0_0}'
|
|
|
2672 #end if
|
|
|
2673
|
|
|
2674 #end if
|
|
|
2675
|
|
|
2676 #if str($CONDITIONAL_ref_allele.CONDITIONAL_SELECT_ref_allele) == "set":
|
|
|
2677 --ref-allele
|
|
|
2678
|
|
|
2679
|
|
|
2680 #if $str($CONDITIONAL_ref_allele.ref_allele_MOD_0_0):
|
|
|
2681 '${CONDITIONAL_ref_allele.ref_allele_MOD_0_0}'
|
|
|
2682 #end if
|
|
|
2683
|
|
|
2684 #if $CONDITIONAL_ref_allele.ref_allele_MOD_1_0:
|
|
|
2685 '${CONDITIONAL_ref_allele.ref_allele_MOD_1_0}'
|
|
|
2686 #end if
|
|
|
2687
|
|
|
2688 #if $str($CONDITIONAL_ref_allele.ref_allele_MOD_2_0):
|
|
|
2689 '${CONDITIONAL_ref_allele.ref_allele_MOD_2_0}'
|
|
|
2690 #end if
|
|
|
2691
|
|
|
2692 #if $str($CONDITIONAL_ref_allele.ref_allele_MOD_3_0):
|
|
|
2693 '${CONDITIONAL_ref_allele.ref_allele_MOD_3_0}'
|
|
|
2694 #end if
|
|
|
2695
|
|
|
2696 #if $str($CONDITIONAL_ref_allele.ref_allele_MOD_4_0):
|
|
|
2697 '${CONDITIONAL_ref_allele.ref_allele_MOD_4_0}'
|
|
|
2698 #end if
|
|
|
2699
|
|
|
2700 #end if
|
|
|
2701
|
|
|
2702 #if str($CONDITIONAL_alt1_allele.CONDITIONAL_SELECT_alt1_allele) == "set":
|
|
|
2703 --alt1-allele
|
|
|
2704
|
|
|
2705
|
|
|
2706 #if $str($CONDITIONAL_alt1_allele.alt1_allele_MOD_0_0):
|
|
|
2707 '${CONDITIONAL_alt1_allele.alt1_allele_MOD_0_0}'
|
|
|
2708 #end if
|
|
|
2709
|
|
|
2710 #if $CONDITIONAL_alt1_allele.alt1_allele_MOD_1_0:
|
|
|
2711 '${CONDITIONAL_alt1_allele.alt1_allele_MOD_1_0}'
|
|
|
2712 #end if
|
|
|
2713
|
|
|
2714 #if $str($CONDITIONAL_alt1_allele.alt1_allele_MOD_2_0):
|
|
|
2715 '${CONDITIONAL_alt1_allele.alt1_allele_MOD_2_0}'
|
|
|
2716 #end if
|
|
|
2717
|
|
|
2718 #if $str($CONDITIONAL_alt1_allele.alt1_allele_MOD_3_0):
|
|
|
2719 '${CONDITIONAL_alt1_allele.alt1_allele_MOD_3_0}'
|
|
|
2720 #end if
|
|
|
2721
|
|
|
2722 #if $str($CONDITIONAL_alt1_allele.alt1_allele_MOD_4_0):
|
|
|
2723 '${CONDITIONAL_alt1_allele.alt1_allele_MOD_4_0}'
|
|
|
2724 #end if
|
|
|
2725
|
|
|
2726 #end if
|
|
|
2727
|
|
|
2728 #if str($CONDITIONAL_ref_from_fa.CONDITIONAL_SELECT_ref_from_fa) == "set":
|
|
|
2729 --ref-from-fa
|
|
|
2730
|
|
|
2731
|
|
|
2732 #if $str($CONDITIONAL_ref_from_fa.ref_from_fa_MOD_0_0):
|
|
|
2733 '${CONDITIONAL_ref_from_fa.ref_from_fa_MOD_0_0}'
|
|
|
2734 #end if
|
|
|
2735
|
|
|
2736 #end if
|
|
|
2737
|
|
|
2738 #if str($CONDITIONAL_normalize.CONDITIONAL_SELECT_normalize) == "set":
|
|
|
2739 --normalize
|
|
|
2740
|
|
|
2741
|
|
|
2742 #if $str($CONDITIONAL_normalize.normalize_MOD_0_0):
|
|
|
2743 '${CONDITIONAL_normalize.normalize_MOD_0_0}'
|
|
|
2744 #end if
|
|
|
2745
|
|
|
2746 #end if
|
|
|
2747
|
|
|
2748 #if str($CONDITIONAL_indiv_sort.CONDITIONAL_SELECT_indiv_sort) == "set":
|
|
|
2749 --indiv-sort
|
|
|
2750
|
|
|
2751
|
|
|
2752 #if $str($CONDITIONAL_indiv_sort.indiv_sort_MOD_0_0):
|
|
|
2753 '${CONDITIONAL_indiv_sort.indiv_sort_MOD_0_0}'
|
|
|
2754 #end if
|
|
|
2755
|
|
|
2756 #if $CONDITIONAL_indiv_sort.indiv_sort_MOD_1_0:
|
|
|
2757 '${CONDITIONAL_indiv_sort.indiv_sort_MOD_1_0}'
|
|
|
2758 #end if
|
|
|
2759
|
|
|
2760 #end if
|
|
|
2761
|
|
|
2762 #if str($CONDITIONAL_king_table_filter.CONDITIONAL_SELECT_king_table_filter) == "set":
|
|
|
2763 --king-table-filter
|
|
|
2764
|
|
|
2765
|
|
|
2766 #if $str($CONDITIONAL_king_table_filter.king_table_filter_MOD_0_0):
|
|
|
2767 '${CONDITIONAL_king_table_filter.king_table_filter_MOD_0_0}'
|
|
|
2768 #end if
|
|
|
2769
|
|
|
2770 #end if
|
|
|
2771
|
|
|
2772 #if str($CONDITIONAL_king_table_subset.CONDITIONAL_SELECT_king_table_subset) == "set":
|
|
|
2773 --king-table-subset
|
|
|
2774
|
|
|
2775
|
|
|
2776 #if $CONDITIONAL_king_table_subset.king_table_subset_MOD_0_0:
|
|
|
2777 '${CONDITIONAL_king_table_subset.king_table_subset_MOD_0_0}'
|
|
|
2778 #end if
|
|
|
2779
|
|
|
2780 #if $str($CONDITIONAL_king_table_subset.king_table_subset_MOD_1_0):
|
|
|
2781 '${CONDITIONAL_king_table_subset.king_table_subset_MOD_1_0}'
|
|
|
2782 #end if
|
|
|
2783
|
|
|
2784 #end if
|
|
|
2785
|
|
|
2786 #if str($CONDITIONAL_condition.CONDITIONAL_SELECT_condition) == "set":
|
|
|
2787 --condition
|
|
|
2788
|
|
|
2789
|
|
|
2790 #if $str($CONDITIONAL_condition.condition_MOD_0_0):
|
|
|
2791 '${CONDITIONAL_condition.condition_MOD_0_0}'
|
|
|
2792 #end if
|
|
|
2793
|
|
|
2794 #if $str($CONDITIONAL_condition.CONDITIONAL_condition_MOD_1.CONDITIONAL_SELECT_condition_MOD_1) == 'from_list'
|
|
|
2795 '${CONDITIONAL_condition.CONDITIONAL_condition_MOD_1.condition_MOD_1}'
|
|
|
2796 #end if
|
|
|
2797
|
|
|
2798
|
|
|
2799 #if $str($CONDITIONAL_condition.condition_MOD_2_0):
|
|
|
2800 '${CONDITIONAL_condition.condition_MOD_2_0}'
|
|
|
2801 #end if
|
|
|
2802
|
|
|
2803 #end if
|
|
|
2804
|
|
|
2805 #if str($CONDITIONAL_condition_list.CONDITIONAL_SELECT_condition_list) == "set":
|
|
|
2806 --condition-list
|
|
|
2807
|
|
|
2808
|
|
|
2809 #if $CONDITIONAL_condition_list.condition_list_MOD_0_0:
|
|
|
2810 '${CONDITIONAL_condition_list.condition_list_MOD_0_0}'
|
|
|
2811 #end if
|
|
|
2812
|
|
|
2813 #if $str($CONDITIONAL_condition_list.CONDITIONAL_condition_list_MOD_1.CONDITIONAL_SELECT_condition_list_MOD_1) == 'from_list'
|
|
|
2814 '${CONDITIONAL_condition_list.CONDITIONAL_condition_list_MOD_1.condition_list_MOD_1}'
|
|
|
2815 #end if
|
|
|
2816
|
|
|
2817
|
|
|
2818 #if $str($CONDITIONAL_condition_list.condition_list_MOD_2_0):
|
|
|
2819 '${CONDITIONAL_condition_list.condition_list_MOD_2_0}'
|
|
|
2820 #end if
|
|
|
2821
|
|
|
2822 #end if
|
|
|
2823
|
|
|
2824 #if str($CONDITIONAL_parameters.CONDITIONAL_SELECT_parameters) == "set":
|
|
|
2825 --parameters
|
|
|
2826
|
|
|
2827
|
|
|
2828 #if $str($CONDITIONAL_parameters.parameters_MOD_0_0):
|
|
|
2829 '${CONDITIONAL_parameters.parameters_MOD_0_0}'
|
|
|
2830 #end if
|
|
|
2831
|
|
|
2832 #end if
|
|
|
2833
|
|
|
2834 #if str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_OVERLOADED_SELECT_tests) == "form_0":
|
|
|
2835 #if str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_tests.CONDITIONAL_SELECT_tests) == "set":
|
|
|
2836 --tests
|
|
|
2837
|
|
|
2838 #if $str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_tests.tests_MOD_0_0):
|
|
|
2839 '${CONDITIONAL_OVERLOADED_tests.CONDITIONAL_tests.tests_MOD_0_0}'
|
|
|
2840 #end if
|
|
|
2841 #end if
|
|
|
2842 #end if
|
|
|
2843
|
|
|
2844 #if str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_OVERLOADED_SELECT_tests) == "form_1":
|
|
|
2845 #if str($CONDITIONAL_OVERLOADED_tests.CONDITIONAL_tests.CONDITIONAL_SELECT_tests) == "set":
|
|
|
2846 --tests
|
|
|
2847
|
|
|
2848 #end if
|
|
|
2849 #end if
|
|
|
2850
|
|
|
2851 #if str($CONDITIONAL_vif.CONDITIONAL_SELECT_vif) == "set":
|
|
|
2852 --vif
|
|
|
2853
|
|
|
2854
|
|
|
2855 #if $str($CONDITIONAL_vif.vif_MOD_0_0):
|
|
|
2856 '${CONDITIONAL_vif.vif_MOD_0_0}'
|
|
|
2857 #end if
|
|
|
2858
|
|
|
2859 #end if
|
|
|
2860
|
|
|
2861 #if str($CONDITIONAL_max_corr.CONDITIONAL_SELECT_max_corr) == "set":
|
|
|
2862 --max-corr
|
|
|
2863
|
|
|
2864
|
|
|
2865 #if $str($CONDITIONAL_max_corr.max_corr_MOD_0_0):
|
|
|
2866 '${CONDITIONAL_max_corr.max_corr_MOD_0_0}'
|
|
|
2867 #end if
|
|
|
2868
|
|
|
2869 #end if
|
|
|
2870
|
|
|
2871 #if str($CONDITIONAL_xchr_model.CONDITIONAL_SELECT_xchr_model) == "set":
|
|
|
2872 --xchr-model
|
|
|
2873
|
|
|
2874
|
|
|
2875 #if $str($CONDITIONAL_xchr_model.xchr_model_MOD_0_0):
|
|
|
2876 '${CONDITIONAL_xchr_model.xchr_model_MOD_0_0}'
|
|
|
2877 #end if
|
|
|
2878
|
|
|
2879 #end if
|
|
|
2880
|
|
|
2881 #if str($CONDITIONAL_adjust.CONDITIONAL_SELECT_adjust) == "set":
|
|
|
2882 --adjust
|
|
|
2883
|
|
|
2884
|
|
|
2885 #if $str($CONDITIONAL_adjust.adjust_MOD_0_0):
|
|
|
2886 '${CONDITIONAL_adjust.adjust_MOD_0_0}'
|
|
|
2887 #end if
|
|
|
2888
|
|
|
2889 #if $str($CONDITIONAL_adjust.adjust_MOD_1_0):
|
|
|
2890 '${CONDITIONAL_adjust.adjust_MOD_1_0}'
|
|
|
2891 #end if
|
|
|
2892
|
|
|
2893 #if $str($CONDITIONAL_adjust.adjust_MOD_2_0):
|
|
|
2894 '${CONDITIONAL_adjust.adjust_MOD_2_0}'
|
|
|
2895 #end if
|
|
|
2896
|
|
|
2897 #if $str($CONDITIONAL_adjust.adjust_MOD_3_0):
|
|
|
2898 '${CONDITIONAL_adjust.adjust_MOD_3_0}'
|
|
|
2899 #end if
|
|
|
2900
|
|
|
2901 #end if
|
|
|
2902
|
|
|
2903 #if str($CONDITIONAL_lambda.CONDITIONAL_SELECT_lambda) == "set":
|
|
|
2904 --lambda
|
|
|
2905
|
|
|
2906
|
|
|
2907 #end if
|
|
|
2908
|
|
|
2909 #if str($CONDITIONAL_adjust_chr_field.CONDITIONAL_SELECT_adjust_chr_field) == "set":
|
|
|
2910 --adjust-chr-field
|
|
|
2911
|
|
|
2912
|
|
|
2913 #if $str($CONDITIONAL_adjust_chr_field.adjust_chr_field_MOD_0_0):
|
|
|
2914 '${CONDITIONAL_adjust_chr_field.adjust_chr_field_MOD_0_0}'
|
|
|
2915 #end if
|
|
|
2916
|
|
|
2917 #end if
|
|
|
2918
|
|
|
2919 #if str($CONDITIONAL_adjust_pos_field.CONDITIONAL_SELECT_adjust_pos_field) == "set":
|
|
|
2920 --adjust-pos-field
|
|
|
2921
|
|
|
2922
|
|
|
2923 #if $str($CONDITIONAL_adjust_pos_field.adjust_pos_field_MOD_0_0):
|
|
|
2924 '${CONDITIONAL_adjust_pos_field.adjust_pos_field_MOD_0_0}'
|
|
|
2925 #end if
|
|
|
2926
|
|
|
2927 #end if
|
|
|
2928
|
|
|
2929 #if str($CONDITIONAL_adjust_id_field.CONDITIONAL_SELECT_adjust_id_field) == "set":
|
|
|
2930 --adjust-id-field
|
|
|
2931
|
|
|
2932
|
|
|
2933 #if $str($CONDITIONAL_adjust_id_field.adjust_id_field_MOD_0_0):
|
|
|
2934 '${CONDITIONAL_adjust_id_field.adjust_id_field_MOD_0_0}'
|
|
|
2935 #end if
|
|
|
2936
|
|
|
2937 #end if
|
|
|
2938
|
|
|
2939 #if str($CONDITIONAL_adjust_ref_field.CONDITIONAL_SELECT_adjust_ref_field) == "set":
|
|
|
2940 --adjust-ref-field
|
|
|
2941
|
|
|
2942
|
|
|
2943 #if $str($CONDITIONAL_adjust_ref_field.adjust_ref_field_MOD_0_0):
|
|
|
2944 '${CONDITIONAL_adjust_ref_field.adjust_ref_field_MOD_0_0}'
|
|
|
2945 #end if
|
|
|
2946
|
|
|
2947 #end if
|
|
|
2948
|
|
|
2949 #if str($CONDITIONAL_adjust_alt_field.CONDITIONAL_SELECT_adjust_alt_field) == "set":
|
|
|
2950 --adjust-alt-field
|
|
|
2951
|
|
|
2952
|
|
|
2953 #if $str($CONDITIONAL_adjust_alt_field.adjust_alt_field_MOD_0_0):
|
|
|
2954 '${CONDITIONAL_adjust_alt_field.adjust_alt_field_MOD_0_0}'
|
|
|
2955 #end if
|
|
|
2956
|
|
|
2957 #end if
|
|
|
2958
|
|
|
2959 #if str($CONDITIONAL_adjust_a1_field.CONDITIONAL_SELECT_adjust_a1_field) == "set":
|
|
|
2960 --adjust-a1-field
|
|
|
2961
|
|
|
2962
|
|
|
2963 #if $str($CONDITIONAL_adjust_a1_field.adjust_a1_field_MOD_0_0):
|
|
|
2964 '${CONDITIONAL_adjust_a1_field.adjust_a1_field_MOD_0_0}'
|
|
|
2965 #end if
|
|
|
2966
|
|
|
2967 #end if
|
|
|
2968
|
|
|
2969 #if str($CONDITIONAL_adjust_test_field.CONDITIONAL_SELECT_adjust_test_field) == "set":
|
|
|
2970 --adjust-test-field
|
|
|
2971
|
|
|
2972
|
|
|
2973 #if $str($CONDITIONAL_adjust_test_field.adjust_test_field_MOD_0_0):
|
|
|
2974 '${CONDITIONAL_adjust_test_field.adjust_test_field_MOD_0_0}'
|
|
|
2975 #end if
|
|
|
2976
|
|
|
2977 #end if
|
|
|
2978
|
|
|
2979 #if str($CONDITIONAL_adjust_p_field.CONDITIONAL_SELECT_adjust_p_field) == "set":
|
|
|
2980 --adjust-p-field
|
|
|
2981
|
|
|
2982
|
|
|
2983 #if $str($CONDITIONAL_adjust_p_field.adjust_p_field_MOD_0_0):
|
|
|
2984 '${CONDITIONAL_adjust_p_field.adjust_p_field_MOD_0_0}'
|
|
|
2985 #end if
|
|
|
2986
|
|
|
2987 #end if
|
|
|
2988
|
|
|
2989 #if str($CONDITIONAL_ci.CONDITIONAL_SELECT_ci) == "set":
|
|
|
2990 --ci
|
|
|
2991
|
|
|
2992
|
|
|
2993 #if $str($CONDITIONAL_ci.ci_MOD_0_0):
|
|
|
2994 '${CONDITIONAL_ci.ci_MOD_0_0}'
|
|
|
2995 #end if
|
|
|
2996
|
|
|
2997 #end if
|
|
|
2998
|
|
|
2999 #if str($CONDITIONAL_pfilter.CONDITIONAL_SELECT_pfilter) == "set":
|
|
|
3000 --pfilter
|
|
|
3001
|
|
|
3002
|
|
|
3003 #if $str($CONDITIONAL_pfilter.pfilter_MOD_0_0):
|
|
|
3004 '${CONDITIONAL_pfilter.pfilter_MOD_0_0}'
|
|
|
3005 #end if
|
|
|
3006
|
|
|
3007 #end if
|
|
|
3008
|
|
|
3009 #if str($CONDITIONAL_score_col_nums.CONDITIONAL_SELECT_score_col_nums) == "set":
|
|
|
3010 --score-col-nums
|
|
|
3011
|
|
|
3012
|
|
|
3013 #if $str($CONDITIONAL_score_col_nums.score_col_nums_MOD_0_0):
|
|
|
3014 '${CONDITIONAL_score_col_nums.score_col_nums_MOD_0_0}'
|
|
|
3015 #end if
|
|
|
3016
|
|
|
3017 #end if
|
|
|
3018
|
|
|
3019 #if str($CONDITIONAL_q_score_range.CONDITIONAL_SELECT_q_score_range) == "set":
|
|
|
3020 --q-score-range
|
|
|
3021
|
|
|
3022
|
|
|
3023 #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_0_0):
|
|
|
3024 '${CONDITIONAL_q_score_range.q_score_range_MOD_0_0}'
|
|
|
3025 #end if
|
|
|
3026
|
|
|
3027 #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_1_0):
|
|
|
3028 '${CONDITIONAL_q_score_range.q_score_range_MOD_1_0}'
|
|
|
3029 #end if
|
|
|
3030
|
|
|
3031 #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_2_0):
|
|
|
3032 '${CONDITIONAL_q_score_range.q_score_range_MOD_2_0}'
|
|
|
3033 #end if
|
|
|
3034
|
|
|
3035 #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_3_0):
|
|
|
3036 '${CONDITIONAL_q_score_range.q_score_range_MOD_3_0}'
|
|
|
3037 #end if
|
|
|
3038
|
|
|
3039 #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_4_0):
|
|
|
3040 '${CONDITIONAL_q_score_range.q_score_range_MOD_4_0}'
|
|
|
3041 #end if
|
|
|
3042
|
|
|
3043 #if $str($CONDITIONAL_q_score_range.q_score_range_MOD_5_0):
|
|
|
3044 '${CONDITIONAL_q_score_range.q_score_range_MOD_5_0}'
|
|
|
3045 #end if
|
|
|
3046
|
|
|
3047 #end if
|
|
|
3048
|
|
|
3049 #if str($CONDITIONAL_vscore_col_nums.CONDITIONAL_SELECT_vscore_col_nums) == "set":
|
|
|
3050 --vscore-col-nums
|
|
|
3051
|
|
|
3052
|
|
|
3053 #if $str($CONDITIONAL_vscore_col_nums.vscore_col_nums_MOD_0_0):
|
|
|
3054 '${CONDITIONAL_vscore_col_nums.vscore_col_nums_MOD_0_0}'
|
|
|
3055 #end if
|
|
|
3056
|
|
|
3057 #end if
|
|
|
3058
|
|
|
3059 #if str($CONDITIONAL_memory.CONDITIONAL_SELECT_memory) == "set":
|
|
|
3060 --memory
|
|
|
3061
|
|
|
3062
|
|
|
3063 #if $str($CONDITIONAL_memory.memory_MOD_0_0):
|
|
|
3064 '${CONDITIONAL_memory.memory_MOD_0_0}'
|
|
|
3065 #end if
|
|
|
3066
|
|
|
3067 #if $str($CONDITIONAL_memory.memory_MOD_1_0):
|
|
|
3068 '${CONDITIONAL_memory.memory_MOD_1_0}'
|
|
|
3069 #end if
|
|
|
3070
|
|
|
3071 #end if
|
|
|
3072
|
|
|
3073 #if str($CONDITIONAL_threads.CONDITIONAL_SELECT_threads) == "set":
|
|
|
3074 --threads
|
|
|
3075
|
|
|
3076
|
|
|
3077 #if $str($CONDITIONAL_threads.threads_MOD_0_0):
|
|
|
3078 '${CONDITIONAL_threads.threads_MOD_0_0}'
|
|
|
3079 #end if
|
|
|
3080
|
|
|
3081 #end if
|
|
|
3082
|
|
|
3083 #if str($CONDITIONAL_d.CONDITIONAL_SELECT_d) == "set":
|
|
|
3084 --d
|
|
|
3085
|
|
|
3086
|
|
|
3087 #if $str($CONDITIONAL_d.d_MOD_0_0):
|
|
|
3088 '${CONDITIONAL_d.d_MOD_0_0}'
|
|
|
3089 #end if
|
|
|
3090
|
|
|
3091 #end if
|
|
|
3092
|
|
|
3093 #if str($CONDITIONAL_seed.CONDITIONAL_SELECT_seed) == "set":
|
|
|
3094 --seed
|
|
|
3095
|
|
|
3096
|
|
|
3097 #if $str($CONDITIONAL_seed.seed_MOD_0_0):
|
|
|
3098 '${CONDITIONAL_seed.seed_MOD_0_0}'
|
|
|
3099 #end if
|
|
|
3100
|
|
|
3101 #end if
|
|
|
3102
|
|
|
3103 #if str($CONDITIONAL_output_min_p.CONDITIONAL_SELECT_output_min_p) == "set":
|
|
|
3104 --output-min-p
|
|
|
3105
|
|
|
3106
|
|
|
3107 #if $str($CONDITIONAL_output_min_p.output_min_p_MOD_0_0):
|
|
|
3108 '${CONDITIONAL_output_min_p.output_min_p_MOD_0_0}'
|
|
|
3109 #end if
|
|
|
3110
|
|
|
3111 #end if
|
|
|
3112
|
|
|
3113 #if str($CONDITIONAL_debug.CONDITIONAL_SELECT_debug) == "set":
|
|
|
3114 --debug
|
|
|
3115
|
|
|
3116
|
|
|
3117 #end if
|
|
|
3118
|
|
|
3119 #if str($CONDITIONAL_randmem.CONDITIONAL_SELECT_randmem) == "set":
|
|
|
3120 --randmem
|
|
|
3121
|
|
|
3122
|
|
|
3123 #end if
|
|
|
3124
|
|
|
3125 #if str($CONDITIONAL_warning_errcode.CONDITIONAL_SELECT_warning_errcode) == "set":
|
|
|
3126 --warning-errcode
|
|
|
3127
|
|
|
3128
|
|
|
3129 #end if
|
|
|
3130
|
|
|
3131 #if str($CONDITIONAL_zst_level.CONDITIONAL_SELECT_zst_level) == "set":
|
|
|
3132 --zst-level
|
|
|
3133
|
|
|
3134
|
|
|
3135 #if $str($CONDITIONAL_zst_level.zst_level_MOD_0_0):
|
|
|
3136 '${CONDITIONAL_zst_level.zst_level_MOD_0_0}'
|
|
|
3137 #end if
|
|
|
3138
|
|
|
3139 #end if
|
|
|
3140 ]]></command>
|
|
|
3141 <inputs>
|
|
|
3142 <conditional name="CONDITIONAL_pfile">
|
|
|
3143 <param name="CONDITIONAL_SELECT_pfile" type="select" label="Set Pfile" help="Specify .pgen + .pvar[.zst] + .psam prefix. " argument="--pfile">
|
|
|
3144 <option value="no_set" selected="True">Don't set</option>
|
|
|
3145 <option value="set">Set value(s)</option>
|
|
|
3146 </param>
|
|
|
3147 <when value="no_set">
|
|
|
3148 </when>
|
|
|
3149 <when value="set">
|
|
|
3150
|
|
|
3151 <param name="pfile_MOD_0_0" type="text" label="prefix" value="" optional="True" argument="prefix" help=""/>
|
|
|
3152 <param name="pfile_MOD_1_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/>
|
|
|
3153 </when>
|
|
|
3154 </conditional>
|
|
|
3155 <conditional name="CONDITIONAL_pgen">
|
|
|
3156 <param name="CONDITIONAL_SELECT_pgen" type="select" label="Set Pgen" help="Specify full name of .pgen/.bed file. " argument="--pgen">
|
|
|
3157 <option value="no_set" selected="True">Don't set</option>
|
|
|
3158 <option value="set">Set value(s)</option>
|
|
|
3159 </param>
|
|
|
3160 <when value="no_set">
|
|
|
3161 </when>
|
|
|
3162 <when value="set">
|
|
|
3163
|
|
|
3164 <param name="pgen_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
3165 </when>
|
|
|
3166 </conditional>
|
|
|
3167 <conditional name="CONDITIONAL_pvar">
|
|
|
3168 <param name="CONDITIONAL_SELECT_pvar" type="select" label="Set Pvar" help="Specify full name of .pvar/.bim file. " argument="--pvar">
|
|
|
3169 <option value="no_set" selected="True">Don't set</option>
|
|
|
3170 <option value="set">Set value(s)</option>
|
|
|
3171 </param>
|
|
|
3172 <when value="no_set">
|
|
|
3173 </when>
|
|
|
3174 <when value="set">
|
|
|
3175
|
|
|
3176 <param name="pvar_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
3177 </when>
|
|
|
3178 </conditional>
|
|
|
3179 <conditional name="CONDITIONAL_psam">
|
|
|
3180 <param name="CONDITIONAL_SELECT_psam" type="select" label="Set Psam" help="Specify full name of .psam/.fam file. " argument="--psam">
|
|
|
3181 <option value="no_set" selected="True">Don't set</option>
|
|
|
3182 <option value="set">Set value(s)</option>
|
|
|
3183 </param>
|
|
|
3184 <when value="no_set">
|
|
|
3185 </when>
|
|
|
3186 <when value="set">
|
|
|
3187
|
|
|
3188 <param name="psam_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
3189 </when>
|
|
|
3190 </conditional>
|
|
|
3191 <conditional name="CONDITIONAL_bpfile">
|
|
|
3192 <param name="CONDITIONAL_SELECT_bpfile" type="select" label="Set Bpfile" help="Specify .pgen + .bim[.zst] + .fam prefix. " argument="--bpfile">
|
|
|
3193 <option value="no_set" selected="True">Don't set</option>
|
|
|
3194 <option value="set">Set value(s)</option>
|
|
|
3195 </param>
|
|
|
3196 <when value="no_set">
|
|
|
3197 </when>
|
|
|
3198 <when value="set">
|
|
|
3199
|
|
|
3200 <param name="bpfile_MOD_0_0" type="text" label="prefix" value="" optional="True" argument="prefix" help=""/>
|
|
|
3201 <param name="bpfile_MOD_1_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/>
|
|
|
3202 </when>
|
|
|
3203 </conditional>
|
|
|
3204 <conditional name="CONDITIONAL_keep_autoconv">
|
|
|
3205 <param name="CONDITIONAL_SELECT_keep_autoconv" type="select" label="Set Keep autoconv" help="When importing non-PLINK-binary data, don't delete autogenerated binary fileset at end of run. " argument="--keep-autoconv">
|
|
|
3206 <option value="no_set" selected="True">Don't set</option>
|
|
|
3207 <option value="set">Set value(s)</option>
|
|
|
3208 </param>
|
|
|
3209 <when value="no_set">
|
|
|
3210 </when>
|
|
|
3211 <when value="set">
|
|
|
3212
|
|
|
3213 </when>
|
|
|
3214 </conditional>
|
|
|
3215 <conditional name="CONDITIONAL_no_fid">
|
|
|
3216 <param name="CONDITIONAL_SELECT_no_fid" type="select" label="Set No fid" help=".fam file does not contain column 1 (family ID). " argument="--no-fid">
|
|
|
3217 <option value="no_set" selected="True">Don't set</option>
|
|
|
3218 <option value="set">Set value(s)</option>
|
|
|
3219 </param>
|
|
|
3220 <when value="no_set">
|
|
|
3221 </when>
|
|
|
3222 <when value="set">
|
|
|
3223
|
|
|
3224 </when>
|
|
|
3225 </conditional>
|
|
|
3226 <conditional name="CONDITIONAL_no_parents">
|
|
|
3227 <param name="CONDITIONAL_SELECT_no_parents" type="select" label="Set No parents" help=".fam file does not contain columns 3-4 (parents). " argument="--no-parents">
|
|
|
3228 <option value="no_set" selected="True">Don't set</option>
|
|
|
3229 <option value="set">Set value(s)</option>
|
|
|
3230 </param>
|
|
|
3231 <when value="no_set">
|
|
|
3232 </when>
|
|
|
3233 <when value="set">
|
|
|
3234
|
|
|
3235 </when>
|
|
|
3236 </conditional>
|
|
|
3237 <conditional name="CONDITIONAL_no_sex">
|
|
|
3238 <param name="CONDITIONAL_SELECT_no_sex" type="select" label="Set No sex" help=".fam file does not contain column 5 (sex). " argument="--no-sex">
|
|
|
3239 <option value="no_set" selected="True">Don't set</option>
|
|
|
3240 <option value="set">Set value(s)</option>
|
|
|
3241 </param>
|
|
|
3242 <when value="no_set">
|
|
|
3243 </when>
|
|
|
3244 <when value="set">
|
|
|
3245
|
|
|
3246 </when>
|
|
|
3247 </conditional>
|
|
|
3248 <conditional name="CONDITIONAL_vcf">
|
|
|
3249 <param name="CONDITIONAL_SELECT_vcf" type="select" label="Set Vcf" help="" argument="--vcf">
|
|
|
3250 <option value="no_set" selected="True">Don't set</option>
|
|
|
3251 <option value="set">Set value(s)</option>
|
|
|
3252 </param>
|
|
|
3253 <when value="no_set">
|
|
|
3254 </when>
|
|
|
3255 <when value="set">
|
|
|
3256
|
|
|
3257 <param name="vcf_MOD_0_0" type="data" format="vcf" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
3258 <param name="vcf_MOD_1_0" type="text" label="'dosage='<field>" value="" optional="False" argument="'dosage='<field>" help=""/>
|
|
|
3259 </when>
|
|
|
3260 </conditional>
|
|
|
3261 <conditional name="CONDITIONAL_bcf">
|
|
|
3262 <param name="CONDITIONAL_SELECT_bcf" type="select" label="Set Bcf" help="Specify full name of .vcf{|.gz|.zst} or BCF2 file to import. * These can be used with --psam/--fam. * By default, dosage information is not imported. To import the GP field (must be VCFv4.3-style 0..1, one probability per possible genotype), add 'dosage=GP' (or 'dosage=GP-force', see below). To import Minimac3-style DS+HDS phased dosage, add 'dosage=HDS'. 'dosage=DS' (or anything else for now) causes the named field to be interpreted as a Minimac3-style dosage. Note that, in the dosage=GP case, PLINK 2 collapses the probabilities down to dosages; you cannot use PLINK 2 to losslessly convert VCF FORMAT:GP data to e.g. BGEN format. To make this more obvious, PLINK 2 now errors out when dosage=GP is used on a file with a FORMAT:DS header line and --import-dosage-certainty wasn't specified, since dosage=DS extracts the same information more quickly in this situation. You can suppress this error with 'dosage=GP-force'. In all of these cases, hardcalls are regenerated from scratch from the dosages. As a consequence, variants with no GT field can now be imported; they will be assumed to contain only diploid calls when HDS is also absent." argument="--bcf">
|
|
|
3263 <option value="no_set" selected="True">Don't set</option>
|
|
|
3264 <option value="set">Set value(s)</option>
|
|
|
3265 </param>
|
|
|
3266 <when value="no_set">
|
|
|
3267 </when>
|
|
|
3268 <when value="set">
|
|
|
3269
|
|
|
3270 <param name="bcf_MOD_0_0" type="data" format="bcf" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
3271 <param name="bcf_MOD_1_0" type="text" label="'dosage='<field>" value="" optional="False" argument="'dosage='<field>" help=""/>
|
|
|
3272 </when>
|
|
|
3273 </conditional>
|
|
|
3274 <conditional name="CONDITIONAL_bgen">
|
|
|
3275 <param name="CONDITIONAL_SELECT_bgen" type="select" label="Set Bgen" help="" argument="--bgen">
|
|
|
3276 <option value="no_set" selected="True">Don't set</option>
|
|
|
3277 <option value="set">Set value(s)</option>
|
|
|
3278 </param>
|
|
|
3279 <when value="no_set">
|
|
|
3280 </when>
|
|
|
3281 <when value="set">
|
|
|
3282
|
|
|
3283 <param name="bgen_MOD_0_0" type="data" format="plink.bgen" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
3284 <param name="bgen_MOD_1_0" type="text" label="REF/ALT mode" value="" optional="False" argument="REF/ALT mode" help=""/>
|
|
|
3285 <param name="bgen_MOD_2_0" type="text" label="'snpid-chr'" value="" optional="False" argument="'snpid-chr'" help=""/>
|
|
|
3286 </when>
|
|
|
3287 </conditional>
|
|
|
3288 <conditional name="CONDITIONAL_gen">
|
|
|
3289 <param name="CONDITIONAL_SELECT_gen" type="select" label="Set Gen" help="" argument="--gen">
|
|
|
3290 <option value="no_set" selected="True">Don't set</option>
|
|
|
3291 <option value="set">Set value(s)</option>
|
|
|
3292 </param>
|
|
|
3293 <when value="no_set">
|
|
|
3294 </when>
|
|
|
3295 <when value="set">
|
|
|
3296
|
|
|
3297 <param name="gen_MOD_0_0" type="data" format="plink.gen" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
3298 <param name="gen_MOD_1_0" type="text" label="REF/ALT mode" value="" optional="False" argument="REF/ALT mode" help=""/>
|
|
|
3299 </when>
|
|
|
3300 </conditional>
|
|
|
3301 <conditional name="CONDITIONAL_sample">
|
|
|
3302 <param name="CONDITIONAL_SELECT_sample" type="select" label="Set Sample" help="Specify an Oxford-format dataset to import. --data specifies a .gen[.zst] + .sample pair, while --bgen specifies a BGEN v1.1+ file. * If a BGEN v1.2+ file contains sample IDs, it may be imported without a companion .sample file. * With 'snpid-chr', chromosome codes are read from the 'SNP ID' field instead of the usual chromosome field. * The following REF/ALT modes are supported: 'ref-first': The first allele for each variant is REF. 'ref-last': The last allele for each variant is REF. 'ref-unknown' (default): The last allele for each variant is treated as provisional-REF. This parameter will be required instead of optional in alpha 3." argument="--sample">
|
|
|
3303 <option value="no_set" selected="True">Don't set</option>
|
|
|
3304 <option value="set">Set value(s)</option>
|
|
|
3305 </param>
|
|
|
3306 <when value="no_set">
|
|
|
3307 </when>
|
|
|
3308 <when value="set">
|
|
|
3309
|
|
|
3310 <param name="sample_MOD_0_0" type="data" format="plink.sample" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
3311 </when>
|
|
|
3312 </conditional>
|
|
|
3313 <conditional name="CONDITIONAL_haps">
|
|
|
3314 <param name="CONDITIONAL_SELECT_haps" type="select" label="Set Haps" help="" argument="--haps">
|
|
|
3315 <option value="no_set" selected="True">Don't set</option>
|
|
|
3316 <option value="set">Set value(s)</option>
|
|
|
3317 </param>
|
|
|
3318 <when value="no_set">
|
|
|
3319 </when>
|
|
|
3320 <when value="set">
|
|
|
3321
|
|
|
3322 <param name="haps_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
3323 <conditional name="CONDITIONAL_haps_MOD_1">
|
|
|
3324 <param name="CONDITIONAL_SELECT_haps_MOD_1" type="select" label="How to set Haps">
|
|
|
3325 <option value="no_set" selected="True">Don't set</option>
|
|
|
3326 <option value="from_list">Select from list</option>
|
|
|
3327
|
|
|
3328 </param>
|
|
|
3329 <when value="no_set">
|
|
|
3330 </when>
|
|
|
3331
|
|
|
3332 <when value="from_list">
|
|
|
3333 <param name="haps_MOD_1" type="select" label="Select value">
|
|
1
|
3334 <option value="{ref-first"><![CDATA[{ref-first]]></option>
|
|
|
3335 <option value="ref-last}"><![CDATA[ref-last}]]></option>
|
|
0
|
3336 </param>
|
|
|
3337 </when>
|
|
|
3338 </conditional>
|
|
|
3339 </when>
|
|
|
3340 </conditional>
|
|
|
3341 <conditional name="CONDITIONAL_legend">
|
|
|
3342 <param name="CONDITIONAL_SELECT_legend" type="select" label="Set Legend" help="Specify .haps [+ .legend] file(s) to import. * When --legend is specified, it's assumed that the --haps file doesn't contain header columns. * On chrX, the second male column may contain dummy '-' entries. (However, PLINK 2 currently cannot handle omitted male columns.) * If not used with --sample, new sample IDs are of the form 'per#/per#'." argument="--legend">
|
|
|
3343 <option value="no_set" selected="True">Don't set</option>
|
|
|
3344 <option value="set">Set value(s)</option>
|
|
|
3345 </param>
|
|
|
3346 <when value="no_set">
|
|
|
3347 </when>
|
|
|
3348 <when value="set">
|
|
|
3349
|
|
|
3350 <param name="legend_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
3351 <param name="legend_MOD_1_0" type="text" label="chr code" value="" optional="True" argument="chr code" help=""/>
|
|
|
3352 </when>
|
|
|
3353 </conditional>
|
|
|
3354 <conditional name="CONDITIONAL_map">
|
|
|
3355 <param name="CONDITIONAL_SELECT_map" type="select" label="Set Map" help="Specify full name of .map file. " argument="--map">
|
|
|
3356 <option value="no_set" selected="True">Don't set</option>
|
|
|
3357 <option value="set">Set value(s)</option>
|
|
|
3358 </param>
|
|
|
3359 <when value="no_set">
|
|
|
3360 </when>
|
|
|
3361 <when value="set">
|
|
|
3362
|
|
|
3363 <param name="map_MOD_0_0" type="data" format="plink.map" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
3364 </when>
|
|
|
3365 </conditional>
|
|
|
3366 <conditional name="CONDITIONAL_import_dosage">
|
|
|
3367 <param name="CONDITIONAL_SELECT_import_dosage" type="select" label="Set Import dosage" help="Specify PLINK 1.x-style dosage file to import. * You must also specify a companion .psam/.fam file. * By default, PLINK assumes that the file contains a header line, which has 'SNP' in (1-based) column i+1, 'A1' in column i+j+2, 'A2' in column i+j+3, and sample FID/IIDs starting from column i+j+k+4. (i/j/k are normally zero, but can be changed with 'skip0', 'skip1', and 'skip2' respectively. FID/IID are normally assumed to be separate tokens, but if they're merged into a single token you can specify the delimiter with 'id-delim='.) If such a header line is not present, use the 'noheader' modifier; samples will then be assumed to appear in the same order as they do in the .psam/.fam file. * You may specify a companion .map file. If you do not, * 'single-chr=' can be used to specify that all variants are on the named chromosome. Otherwise, you can use 'chr-col-num=' to read chromosome codes from the given (1-based) column number. * 'pos-col-num=' causes bp coordinates to be read from the given column number. * The 'format=' modifier lets you specify the number of values used to represent each dosage. 'format=1' normally indicates a single 0..2 A1 expected count; 'dose1' modifies this to a 0..1 frequency. 'format=2' indicates a 0..1 homozygous A1 likelihood followed by a 0..1 het likelihood. 'format=3' indicates 0..1 hom A1, 0..1 het, 0..1 hom A2. 'format=infer' (the default) infers the format from the number of columns in the first nonheader line." argument="--import-dosage">
|
|
|
3368 <option value="no_set" selected="True">Don't set</option>
|
|
|
3369 <option value="set">Set value(s)</option>
|
|
|
3370 </param>
|
|
|
3371 <when value="no_set">
|
|
|
3372 </when>
|
|
|
3373 <when value="set">
|
|
|
3374
|
|
|
3375 <param name="import_dosage_MOD_0_0" type="text" label="allele dosage file" value="" optional="True" argument="allele dosage file" help=""/>
|
|
|
3376 <param name="import_dosage_MOD_1_0" type="text" label="'noheader'" value="" optional="False" argument="'noheader'" help=""/>
|
|
|
3377 <param name="import_dosage_MOD_2_0" type="text" label="'id-delim='<char>" value="" optional="False" argument="'id-delim='<char>" help=""/>
|
|
|
3378 <param name="import_dosage_MOD_3_0" type="text" label="'skip0='<i>" value="" optional="False" argument="'skip0='<i>" help=""/>
|
|
|
3379 <param name="import_dosage_MOD_4_0" type="text" label="'skip1='<j>" value="" optional="False" argument="'skip1='<j>" help=""/>
|
|
|
3380 <param name="import_dosage_MOD_5_0" type="text" label="'skip2='<k>" value="" optional="False" argument="'skip2='<k>" help=""/>
|
|
|
3381 <param name="import_dosage_MOD_6_0" type="text" label="'dose1'" value="" optional="False" argument="'dose1'" help=""/>
|
|
|
3382 <param name="import_dosage_MOD_7_0" type="text" label="'format='<m>" value="" optional="False" argument="'format='<m>" help=""/>
|
|
|
3383 <conditional name="CONDITIONAL_import_dosage_MOD_8">
|
|
|
3384 <param name="CONDITIONAL_SELECT_import_dosage_MOD_8" type="select" label="How to set Import dosage">
|
|
|
3385 <option value="no_set" selected="True">Don't set</option>
|
|
|
3386 <option value="from_list">Select from list</option>
|
|
|
3387
|
|
|
3388 </param>
|
|
|
3389 <when value="no_set">
|
|
|
3390 </when>
|
|
|
3391
|
|
|
3392 <when value="from_list">
|
|
|
3393 <param name="import_dosage_MOD_8" type="select" label="Select value">
|
|
1
|
3394 <option value="{ref-first"><![CDATA[{ref-first]]></option>
|
|
|
3395 <option value="ref-last}"><![CDATA[ref-last}]]></option>
|
|
0
|
3396 </param>
|
|
|
3397 </when>
|
|
|
3398 </conditional>
|
|
|
3399 <param name="import_dosage_MOD_9_0" type="text" label="'single-chr='<code>" value="" optional="False" argument="'single-chr='<code>" help=""/>
|
|
|
3400 <param name="import_dosage_MOD_10_0" type="text" label="'chr-col-num='<#>" value="" optional="False" argument="'chr-col-num='<#>" help=""/>
|
|
|
3401 <param name="import_dosage_MOD_11_0" type="text" label="'pos-col-num='<#>" value="" optional="False" argument="'pos-col-num='<#>" help=""/>
|
|
|
3402 </when>
|
|
|
3403 </conditional>
|
|
|
3404 <conditional name="CONDITIONAL_dummy">
|
|
|
3405 <param name="CONDITIONAL_SELECT_dummy" type="select" label="Set Dummy" help="This generates a fake input dataset with the specified number of samples and SNPs. * By default, the missing dosage and phenotype frequencies are zero. These can be changed by providing 3rd and 4th numeric parameters. * By default, allele codes are As and Bs; this can be changed with the 'acgt', '1234', or '12' modifier. * By default, one binary phenotype is generated. 'pheno-ct=' can be used to change the number of phenotypes, and 'scalar-pheno' causes these phenotypes to be normally distributed scalars. * By default, all (nonmissing) dosages are in {0,1,2}. To make some of them take on decimal values, use 'dosage-freq='. (These dosages are affected by --hard-call-threshold and --dosage-erase-threshold.)" argument="--dummy">
|
|
|
3406 <option value="no_set" selected="True">Don't set</option>
|
|
|
3407 <option value="set">Set value(s)</option>
|
|
|
3408 </param>
|
|
|
3409 <when value="no_set">
|
|
|
3410 </when>
|
|
|
3411 <when value="set">
|
|
|
3412
|
|
|
3413 <param name="dummy_MOD_0_0" type="text" label="sample ct" value="" optional="True" argument="sample ct" help=""/>
|
|
|
3414 <param name="dummy_MOD_1_0" type="text" label="SNP ct" value="" optional="True" argument="SNP ct" help=""/>
|
|
|
3415 <param name="dummy_MOD_2_0" type="text" label="missing dosage freq" value="" optional="False" argument="missing dosage freq" help=""/>
|
|
|
3416 <param name="dummy_MOD_3_0" type="text" label="missing pheno freq" value="" optional="False" argument="missing pheno freq" help=""/>
|
|
|
3417 <conditional name="CONDITIONAL_dummy_MOD_4">
|
|
|
3418 <param name="CONDITIONAL_SELECT_dummy_MOD_4" type="select" label="How to set Dummy">
|
|
|
3419 <option value="no_set" selected="True">Don't set</option>
|
|
|
3420 <option value="from_list">Select from list</option>
|
|
|
3421
|
|
|
3422 </param>
|
|
|
3423 <when value="no_set">
|
|
|
3424 </when>
|
|
|
3425
|
|
|
3426 <when value="from_list">
|
|
|
3427 <param name="dummy_MOD_4" type="select" label="Select value">
|
|
1
|
3428 <option value="{acgt"><![CDATA[{acgt]]></option>
|
|
|
3429 <option value="1234"><![CDATA[1234]]></option>
|
|
|
3430 <option value="12}"><![CDATA[12}]]></option>
|
|
0
|
3431 </param>
|
|
|
3432 </when>
|
|
|
3433 </conditional>
|
|
|
3434 <param name="dummy_MOD_5_0" type="text" label="'pheno-ct='<count>" value="" optional="False" argument="'pheno-ct='<count>" help=""/>
|
|
|
3435 <param name="dummy_MOD_6_0" type="text" label="'scalar-pheno'" value="" optional="False" argument="'scalar-pheno'" help=""/>
|
|
|
3436 <param name="dummy_MOD_7_0" type="text" label="'dosage-freq='<rate>" value="" optional="False" argument="'dosage-freq='<rate>" help=""/>
|
|
|
3437 </when>
|
|
|
3438 </conditional>
|
|
|
3439 <conditional name="CONDITIONAL_fa">
|
|
|
3440 <param name="CONDITIONAL_SELECT_fa" type="select" label="Set Fa" help="Specify full name of reference FASTA file. " argument="--fa">
|
|
|
3441 <option value="no_set" selected="True">Don't set</option>
|
|
|
3442 <option value="set">Set value(s)</option>
|
|
|
3443 </param>
|
|
|
3444 <when value="no_set">
|
|
|
3445 </when>
|
|
|
3446 <when value="set">
|
|
|
3447
|
|
|
3448 <param name="fa_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
3449 </when>
|
|
|
3450 </conditional>
|
|
|
3451 <conditional name="CONDITIONAL_rm_dup">
|
|
|
3452 <param name="CONDITIONAL_SELECT_rm_dup" type="select" label="Set Rm dup" help="Remove all but one instance of each duplicate-ID variant (ignoring the missing ID), and (with the 'list' modifier) write a list of duplicated IDs to <output prefix>.rmdup.list. The following modes of operation are supported: * 'error' (default) causes this to error out when there's a genotype data or other mismatch between the records. A list of affected IDs is written to <output prefix>.rmdup.mismatch. * 'retain-mismatch' causes all instances of a duplicate-ID variant to be retained when there's a genotype data or variant info mismatch; otherwise one instance is kept. The .rmdup.mismatch file is also written. * 'exclude-mismatch' removes all instances of duplicate-ID mismatched variants instead. * 'exclude-all' causes all instances of duplicate-ID variants to be removed, even when the actual records are identical. * 'force-first' causes only the first instance of duplicate-ID variants to be kept, under all circumstances." argument="--rm-dup">
|
|
|
3453 <option value="no_set" selected="True">Don't set</option>
|
|
|
3454 <option value="set">Set value(s)</option>
|
|
|
3455 </param>
|
|
|
3456 <when value="no_set">
|
|
|
3457 </when>
|
|
|
3458 <when value="set">
|
|
|
3459
|
|
|
3460 <param name="rm_dup_MOD_0_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/>
|
|
|
3461 <param name="rm_dup_MOD_1_0" type="text" label="'list'" value="" optional="False" argument="'list'" help=""/>
|
|
|
3462 </when>
|
|
|
3463 </conditional>
|
|
|
3464 <conditional name="CONDITIONAL_make_pgen">
|
|
|
3465 <param name="CONDITIONAL_SELECT_make_pgen" type="select" label="Set Make pgen" help="" argument="--make-pgen">
|
|
|
3466 <option value="no_set" selected="True">Don't set</option>
|
|
|
3467 <option value="set">Set value(s)</option>
|
|
|
3468 </param>
|
|
|
3469 <when value="no_set">
|
|
|
3470 </when>
|
|
|
3471 <when value="set">
|
|
|
3472
|
|
|
3473 <param name="make_pgen_MOD_0_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/>
|
|
|
3474 <param name="make_pgen_MOD_1_0" type="text" label="'format='<code>" value="" optional="False" argument="'format='<code>" help=""/>
|
|
|
3475 <param name="make_pgen_MOD_2_0" type="text" label="'trim-alts'" value="" optional="False" argument="'trim-alts'" help=""/>
|
|
|
3476 <param name="make_pgen_MOD_3_0" type="text" label="'erase-phase'" value="" optional="False" argument="'erase-phase'" help=""/>
|
|
|
3477 <param name="make_pgen_MOD_4_0" type="text" label="'erase-dosage'" value="" optional="False" argument="'erase-dosage'" help=""/>
|
|
|
3478 <param name="make_pgen_MOD_5_0" type="text" label="'pvar-cols='<col set descriptor>" value="" optional="False" argument="'pvar-cols='<col set descriptor>" help=""/>
|
|
|
3479 <param name="make_pgen_MOD_6_0" type="text" label="'psam-cols='<col set descriptor>" value="" optional="False" argument="'psam-cols='<col set descriptor>" help=""/>
|
|
|
3480 </when>
|
|
|
3481 </conditional>
|
|
|
3482 <conditional name="CONDITIONAL_make_bpgen">
|
|
|
3483 <param name="CONDITIONAL_SELECT_make_bpgen" type="select" label="Set Make bpgen" help="" argument="--make-bpgen">
|
|
|
3484 <option value="no_set" selected="True">Don't set</option>
|
|
|
3485 <option value="set">Set value(s)</option>
|
|
|
3486 </param>
|
|
|
3487 <when value="no_set">
|
|
|
3488 </when>
|
|
|
3489 <when value="set">
|
|
|
3490
|
|
|
3491 <param name="make_bpgen_MOD_0_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/>
|
|
|
3492 <param name="make_bpgen_MOD_1_0" type="text" label="'format='<code>" value="" optional="False" argument="'format='<code>" help=""/>
|
|
|
3493 <param name="make_bpgen_MOD_2_0" type="text" label="'trim-alts'" value="" optional="False" argument="'trim-alts'" help=""/>
|
|
|
3494 <param name="make_bpgen_MOD_3_0" type="text" label="'erase-phase'" value="" optional="False" argument="'erase-phase'" help=""/>
|
|
|
3495 <param name="make_bpgen_MOD_4_0" type="text" label="'erase-dosage'" value="" optional="False" argument="'erase-dosage'" help=""/>
|
|
|
3496 </when>
|
|
|
3497 </conditional>
|
|
|
3498 <conditional name="CONDITIONAL_make_bed">
|
|
|
3499 <param name="CONDITIONAL_SELECT_make_bed" type="select" label="Set Make bed" help="Create a new PLINK binary fileset (--make-pgen = .pgen + .pvar[.zst] + .psam, --make-bpgen = .pgen + .bim[.zst] + .fam). * Unlike the automatic text-to-binary converters (which only heed chromosome filters), this supports all of PLINK's filtering flags. * The 'vzs' modifier causes the variant file (.pvar/.bim) to be Zstd-compressed. * The 'format' modifier requests an uncompressed fixed-variant-width .pgen file. (These do not directly support multiallelic variants.) The following format code is currently supported: 2: just like .bed, except with an extended (12-byte instead of 3-byte) header containing variant/sample counts, and rotated genotype codes (00 = hom ref, 01 = het, 10 = hom alt, 11 = missing). * The 'erase-phase' and 'erase-dosage' modifiers prevent phase and dosage information from being written to the new .pgen. * The first five columns of a .pvar file are always #CHROM/POS/ID/REF/ALT. Supported optional .pvar column sets are: xheader: All ## header lines (yeah, this is technically not a column), except for possibly FILTER/INFO definitions when those column(s) have been removed. Without this, only the #CHROM header line is kept. maybequal: QUAL. Omitted if all remaining values are missing. qual: Force QUAL column to be written even when empty. maybefilter: FILTER. Omitted if all remaining values are missing. filter: Force FILTER column to be written even when empty. maybeinfo: INFO. Omitted if all remaining values are missing, or if INFO:PR is the only subfield. info: Force INFO column to be written. maybecm: Centimorgan coordinate. Omitted if all remaining values = 0. cm: Force CM column to be written even when empty. The default is xheader,maybequal,maybefilter,maybeinfo,maybecm. * Supported column sets for the .psam file are: maybefid: Family ID, '0' = missing. Omitted if all values missing. fid: Force FID column to be written even when empty. maybesid: Source ID, '0' = missing. Omitted if all values missing. sid: Force SID column to be written even when empty. maybeparents: Father and mother IIDs. Omitted if all values missing. parents: Force PAT and MAT columns to be written even when empty. sex: '1' = male, '2' = female, 'NA' = missing. pheno1: First active phenotype. If none, all column entries are set to the --output-missing-phenotype string. phenos: All active phenotypes, if any. (Can be combined with pheno1 to force at least one phenotype column to be written.) The default is maybefid,maybesid,maybeparents,sex,phenos." argument="--make-bed">
|
|
|
3500 <option value="no_set" selected="True">Don't set</option>
|
|
|
3501 <option value="set">Set value(s)</option>
|
|
|
3502 </param>
|
|
|
3503 <when value="no_set">
|
|
|
3504 </when>
|
|
|
3505 <when value="set">
|
|
|
3506
|
|
|
3507 <param name="make_bed_MOD_0_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/>
|
|
|
3508 <param name="make_bed_MOD_1_0" type="text" label="'trim-alts'" value="" optional="False" argument="'trim-alts'" help=""/>
|
|
|
3509 </when>
|
|
|
3510 </conditional>
|
|
|
3511 <conditional name="CONDITIONAL_make_just_pvar">
|
|
|
3512 <param name="CONDITIONAL_SELECT_make_just_pvar" type="select" label="Set Make just pvar" help="" argument="--make-just-pvar">
|
|
|
3513 <option value="no_set" selected="True">Don't set</option>
|
|
|
3514 <option value="set">Set value(s)</option>
|
|
|
3515 </param>
|
|
|
3516 <when value="no_set">
|
|
|
3517 </when>
|
|
|
3518 <when value="set">
|
|
|
3519
|
|
|
3520 <param name="make_just_pvar_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
3521 <param name="make_just_pvar_MOD_1_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/>
|
|
|
3522 </when>
|
|
|
3523 </conditional>
|
|
|
3524 <conditional name="CONDITIONAL_make_just_psam">
|
|
|
3525 <param name="CONDITIONAL_SELECT_make_just_psam" type="select" label="Set Make just psam" help="" argument="--make-just-psam">
|
|
|
3526 <option value="no_set" selected="True">Don't set</option>
|
|
|
3527 <option value="set">Set value(s)</option>
|
|
|
3528 </param>
|
|
|
3529 <when value="no_set">
|
|
|
3530 </when>
|
|
|
3531 <when value="set">
|
|
|
3532
|
|
|
3533 <param name="make_just_psam_MOD_0_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/>
|
|
|
3534 </when>
|
|
|
3535 </conditional>
|
|
|
3536 <conditional name="CONDITIONAL_make_just_bim">
|
|
|
3537 <param name="CONDITIONAL_SELECT_make_just_bim" type="select" label="Set Make just bim" help="" argument="--make-just-bim">
|
|
|
3538 <option value="no_set" selected="True">Don't set</option>
|
|
|
3539 <option value="set">Set value(s)</option>
|
|
|
3540 </param>
|
|
|
3541 <when value="no_set">
|
|
|
3542 </when>
|
|
|
3543 <when value="set">
|
|
|
3544
|
|
|
3545 <param name="make_just_bim_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
3546 </when>
|
|
|
3547 </conditional>
|
|
|
3548 <param name="make_just_fam" type="boolean" label="Make just fam" truevalue="--make-just-fam" falsevalue="" optional="true" argument="--make-just-fam" help="Variants of --make-pgen/--make-bed which only write a new variant or sample file. These don't always require an input genotype file. USE THESE CAUTIOUSLY. It is very easy to desynchronize your binary genotype data and your sample/variant indexes if you use these commands improperly. If you have any doubt, stick with --make-[b]pgen/--make-bed." checked="False"/>
|
|
|
3549 <conditional name="CONDITIONAL_export">
|
|
|
3550 <param name="CONDITIONAL_SELECT_export" type="select" label="Set Export" help="Create a new fileset with all filters applied. The following output formats are supported: (actually, only A, AD, A-transpose, bgen-1.x, ind-major-bed, haps, hapslegend, oxford, and vcf are implemented for now) * '23': 23andMe 4-column format. This can only be used on a single sample's data (--keep may be handy), and does not support multicharacter allele codes. * 'A': Sample-major additive (0/1/2) coding, suitable for loading from R. If you need uncounted alleles to be named in the header line, add the 'include-alt' modifier. * 'AD': Sample-major additive (0/1/2) + dominant (het=1/hom=0) coding. Also supports 'include-alt'. * 'A-transpose': Variant-major 0/1/2. * 'beagle': Unphased per-autosome .dat and .map files, readable by early BEAGLE versions. * 'beagle-nomap': Single .beagle.dat file. * 'bgen-1.x': Oxford-format .bgen + .sample. For v1.2/v1.3, sample identifiers are stored in the .bgen (with id-delim and id-paste settings applied), and default precision is 16-bit (use the 'bits' modifier to reduce this). * 'bimbam': Regular BIMBAM format. * 'bimbam-1chr': BIMBAM format, with a two-column .pos.txt file. Does not support multiple chromosomes. * 'fastphase': Per-chromosome fastPHASE files, with .chr-<chr #>.phase.inp filename extensions. * 'fastphase-1chr': Single .phase.inp file. Does not support multiple chromosomes. * 'haps', 'hapslegend': Oxford-format .haps + .sample[ + .legend]. All data must be biallelic and phased. When the 'bgz' modifier is present, the .haps file is block-gzipped. * 'HV': Per-chromosome Haploview files, with .chr-<chr #>{.ped,.info} filename extensions. * 'HV-1chr': Single Haploview .ped + .info file pair. Does not support multiple chromosomes. * 'ind-major-bed': PLINK 1 sample-major .bed (+ .bim + .fam). * 'lgen': PLINK 1 long-format (.lgen + .fam + .map), loadable with --lfile. * 'lgen-ref': .lgen + .fam + .map + .ref, loadable with --lfile + --reference. * 'list': Single genotype-based list, up to 4 lines per variant. To omit nonmale genotypes on the Y chromosome, add the 'omit-nonmale-y' modifier. * 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a genotype-based list which omits the most common genotype for each variant. Also supports 'omit-nonmale-y'. * 'oxford': Oxford-format .gen + .sample. When the 'bgz' modifier is present, the .gen file is block-gzipped. * 'ped': PLINK 1 sample-major (.ped + .map), loadable with --file. * 'compound-genotypes': Same as 'ped', except that the space between each pair of same-variant allele codes is removed. * 'structure': Structure-format. * 'transpose': PLINK 1 variant-major (.tped + .tfam), loadable with --tfile. * 'vcf', 'vcf-4.2': VCF (default version 4.3). If PAR1 and PAR2 are present, they are automatically merged with chrX, with proper handling of chromosome codes and male ploidy. When the 'bgz' modifier is present, the VCF file is block-gzipped. The 'id-paste' modifier controls which .psam columns are used to construct sample IDs (choices are maybefid, fid, iid, maybesid, and sid; default is maybefid,iid,maybesid), while the 'id-delim' modifier sets the character between the ID pieces (default '_'). Dosages are not exported unless the 'vcf-dosage=' modifier is present. The following five dosage export modes are supported: 'GP': genotype posterior probabilities (v4.3 only). 'DS': Minimac3-style dosages, omitted for hardcalls. 'DS-force': Minimac3-style dosages, never omit. 'HDS': Minimac3-style phased dosages, omitted for hardcalls and unphased calls. Also includes 'DS' output. 'HDS-force': Always report DS and HDS. In addition, * The '12' modifier causes alt1 alleles to be coded as '1' and ref alleles to be coded as '2', while '01' maps alt1 -> 0 and ref -> 1. * The 'spaces' modifier makes the output space-delimited instead of tab-delimited, whenever both are permitted. * For biallelic formats where it's unspecified whether the reference/major allele should appear first or second, --export defaults to second for compatibility with PLINK 1.9. Use 'ref-first' to change this. (Note that this doesn't apply to the 'A', 'AD', and 'A-transpose' formats; use --export-allele to control which alleles are counted there.)" argument="--export">
|
|
|
3551 <option value="no_set" selected="True">Don't set</option>
|
|
|
3552 <option value="set">Set value(s)</option>
|
|
|
3553 </param>
|
|
|
3554 <when value="no_set">
|
|
|
3555 </when>
|
|
|
3556 <when value="set">
|
|
|
3557
|
|
|
3558 <param name="export_MOD_0_0" type="text" label="output format(s)..." value="" optional="True" argument="output format(s)..." help="Multiple values are allowed"/>
|
|
|
3559 <conditional name="CONDITIONAL_export_MOD_1">
|
|
|
3560 <param name="CONDITIONAL_SELECT_export_MOD_1" type="select" label="How to set Export">
|
|
|
3561 <option value="no_set" selected="True">Don't set</option>
|
|
|
3562 <option value="from_list">Select from list</option>
|
|
|
3563
|
|
|
3564 </param>
|
|
|
3565 <when value="no_set">
|
|
|
3566 </when>
|
|
|
3567
|
|
|
3568 <when value="from_list">
|
|
|
3569 <param name="export_MOD_1" type="select" label="Select value">
|
|
1
|
3570 <option value="{01"><![CDATA[{01]]></option>
|
|
|
3571 <option value="12}"><![CDATA[12}]]></option>
|
|
0
|
3572 </param>
|
|
|
3573 </when>
|
|
|
3574 </conditional>
|
|
|
3575 <param name="export_MOD_2_0" type="text" label="'bgz'" value="" optional="False" argument="'bgz'" help=""/>
|
|
|
3576 <param name="export_MOD_3_0" type="text" label="'id-delim='<char>" value="" optional="False" argument="'id-delim='<char>" help=""/>
|
|
|
3577 <param name="export_MOD_4_0" type="text" label="'id-paste='<column set descriptor>" value="" optional="False" argument="'id-paste='<column set descriptor>" help=""/>
|
|
|
3578 <param name="export_MOD_5_0" type="text" label="'include-alt'" value="" optional="False" argument="'include-alt'" help=""/>
|
|
|
3579 <param name="export_MOD_6_0" type="text" label="'omit-nonmale-y'" value="" optional="False" argument="'omit-nonmale-y'" help=""/>
|
|
|
3580 <param name="export_MOD_7_0" type="text" label="'spaces'" value="" optional="False" argument="'spaces'" help=""/>
|
|
|
3581 <param name="export_MOD_8_0" type="text" label="'vcf-dosage='<field>" value="" optional="False" argument="'vcf-dosage='<field>" help=""/>
|
|
|
3582 <param name="export_MOD_9_0" type="text" label="'ref-first'" value="" optional="False" argument="'ref-first'" help=""/>
|
|
|
3583 <param name="export_MOD_10_0" type="text" label="'bits='<#>" value="" optional="False" argument="'bits='<#>" help=""/>
|
|
|
3584 </when>
|
|
|
3585 </conditional>
|
|
|
3586 <conditional name="CONDITIONAL_freq">
|
|
|
3587 <param name="CONDITIONAL_SELECT_freq" type="select" label="Set Freq" help="['refbins='<comma-separated bin boundaries> | 'refbins-file='<file>] ['alt1bins='<comma-separated bin boundaries> | 'alt1bins-file='<file>] Empirical allele frequency report. By default, only founders are considered. Dosages are taken into account (e.g. heterozygous haploid calls count as 0.5). Supported column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. reffreq: Reference allele frequency/dosage. alt1freq: Alt1 frequency/dosage. altfreq: Comma-separated frequencies/dosages for all alternate alleles. freq: Similar to altfreq, except ref is also included at the start. eq: Comma-separated <allele>=<freq> for all present alleles. (If no alleles are present, the column contains a single '.'.) eqz: Same as eq, except zero-counts are included. alteq/alteqz: Same as eq/eqz, except reference allele is omitted. numeq: 0=<freq>,1=<freq>, etc. Zero-counts are omitted. altnumeq: Same as numeq, except reference allele is omitted. machr2: Unphased MaCH imputation quality metric. minimac3r2: Phased Minimac3 imputation quality. nobs: Number of allele observations. The default is chrom,ref,alt,altfreq,nobs. Additional .afreq.{ref,alt1}.bins (or .acount.{ref,alt1}.bins with 'counts') file(s) are generated when 'refbins='/'refbins-file=' or 'alt1bins='/'alt1bins-file=' is present; these report the total number of frequencies or counts in each left-closed, right-open interval. (If you only want these histogram(s), and not the main report, add 'bins-only'.)" argument="--freq">
|
|
|
3588 <option value="no_set" selected="True">Don't set</option>
|
|
|
3589 <option value="set">Set value(s)</option>
|
|
|
3590 </param>
|
|
|
3591 <when value="no_set">
|
|
|
3592 </when>
|
|
|
3593 <when value="set">
|
|
|
3594
|
|
|
3595 <param name="freq_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
3596 <param name="freq_MOD_1_0" type="text" label="'counts'" value="" optional="False" argument="'counts'" help=""/>
|
|
|
3597 <param name="freq_MOD_2_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/>
|
|
|
3598 <param name="freq_MOD_3_0" type="text" label="'bins-only'" value="" optional="False" argument="'bins-only'" help=""/>
|
|
|
3599 </when>
|
|
|
3600 </conditional>
|
|
|
3601 <conditional name="CONDITIONAL_geno_counts">
|
|
|
3602 <param name="CONDITIONAL_SELECT_geno_counts" type="select" label="Set Geno counts" help="Variant-based hardcall genotype count report (considering both alleles simultaneously in the diploid case). Nonfounders are now included; use --keep-founders if this is a problem. Heterozygous haploid calls are treated as missing. Supported column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. homref: Homozygous-ref count. refalt1: Heterozygous ref-alt1 count. refalt: Comma-separated het ref-altx counts. homalt1: Homozygous-alt1 count. altxy: Comma-separated altx-alty counts, in (1/1)-(1/2)-(2/2)-(1/3)-... order. xy: Similar to altxy, except the reference allele is treated as alt0, and the sequence starts (0/0)-(0/1)-(1/1)-(0/2)-... hapref: Haploid-ref count. hapalt1: Haploid-alt1 count. hapalt: Comma-separated haploid-altx counts. hap: Similar to hapalts, except ref is also included at the start. numeq: 0/0=<hom ref ct>,0/1=<het ref-alt1>,1/1=<hom alt1>,...,0=<hap ref> etc. Zero-counts are omitted. (If all genotypes are missing, the column contains a single '.'.) missing: Number of missing genotypes. nobs: Number of (nonmissing) genotype observations. The default is chrom,ref,alt,homref,refalt,altxy,hapref,hapalt,missing." argument="--geno-counts">
|
|
|
3603 <option value="no_set" selected="True">Don't set</option>
|
|
|
3604 <option value="set">Set value(s)</option>
|
|
|
3605 </param>
|
|
|
3606 <when value="no_set">
|
|
|
3607 </when>
|
|
|
3608 <when value="set">
|
|
|
3609
|
|
|
3610 <param name="geno_counts_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
3611 <param name="geno_counts_MOD_1_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/>
|
|
|
3612 </when>
|
|
|
3613 </conditional>
|
|
|
3614 <conditional name="CONDITIONAL_sample_counts">
|
|
|
3615 <param name="CONDITIONAL_SELECT_sample_counts" type="select" label="Set Sample counts" help="Sample-based hardcall genotype count report. * Unknown-sex samples are treated as female. * Heterozygous haploid calls (MT included) are treated as missing. * As with other PLINK 2 commands, SNPs that have not been left-normalized are counted as non-SNP non-symbolic. (Use e.g. --normalize when that's a problem.) * Supported column sets are: maybefid: FID, if that column was present in the input. fid: Force FID column to be written even when absent in the input. (IID is always present, and positioned here.) maybesid: SID, if that column was present in the input. sid: Force SID column to be written even when absent in the input. sex: '1' = male, '2' = female, 'NA' = missing. hom: Homozygous genotype count. homref: Homozygous-ref genotype count. homalt: Homozygous-alt genotype count. homaltsnp: Homozygous-alt SNP count. het: Heterozygous genotype count. refalt: Heterozygous ref-altx genotype count. het2alt: Heterozygous altx-alty genotype count. hetsnp: Heterozygous SNP count. dipts: Diploid SNP transition count. ts: SNP transition count (excluding chrY for females). diptv: Diploid SNP transversion count. tv: SNP transversion count. dipnonsnpsymb: Diploid non-SNP, non-symbolic count. nonsnpsymb: Non-SNP, non-symbolic count. symbolic: Symbolic variant count. nonsnp: Non-SNP count. dipsingle: Number of singletons relative to this dataset, across just diploid calls. (Note that if the ALT allele in a chrX biallelic variant appears in exactly one female and one male, that counts as a singleton for just the female.) single: Number of singletons relative to this dataset. haprefwfemaley: Haploid-ref count, counting chrY for everyone. hapref: Haploid-ref count, excluding chrY for females. hapaltwfemaley: Haploid-alt count, counting chrY for everyone. hapalt: Haploid-alt count, excluding chrY for females. missingwfemaley: Missing call count, counting chrY for everyone. missing: Missing call count, excluding chrY for females. The default is maybefid,maybesid,homref,homaltsnp,hetsnp,dipts,diptv, dipnonsnpsymb,dipsingle,haprefwfemaley,hapaltwfemaley,missingwfemaley. * The 'hetsnp', 'dipts'/'ts'/'diptv'/'tv', 'dipnonsnpsymb'/'nonsnpsymb', 'symbolic', and 'nonsnp' columns count each ALT allele in a heterozygous altx-alty call separately, since they can be of different subtypes. (I.e. if they are of the same subtype, the corresponding count is incremented by 2.) As a consequence, these columns are unaffected by variant split/join." argument="--sample-counts">
|
|
|
3616 <option value="no_set" selected="True">Don't set</option>
|
|
|
3617 <option value="set">Set value(s)</option>
|
|
|
3618 </param>
|
|
|
3619 <when value="no_set">
|
|
|
3620 </when>
|
|
|
3621 <when value="set">
|
|
|
3622
|
|
|
3623 <param name="sample_counts_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
3624 <param name="sample_counts_MOD_1_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/>
|
|
|
3625 </when>
|
|
|
3626 </conditional>
|
|
|
3627 <conditional name="CONDITIONAL_missing">
|
|
|
3628 <param name="CONDITIONAL_SELECT_missing" type="select" label="Set Missing" help="Generate sample- and variant-based missing data reports (or just one report if 'sample-only'/'variant-only' is specified). As of alpha 2, mixed MT hardcalls appear in the heterozygous haploid stats. Supported column sets in the sample-based report are: maybefid: FID, if that column was present in the input. fid: Force FID column to be written even when absent in the input. (IID is always present, and positioned here.) maybesid: SID, if that column was present in the input. sid: Force SID column to be written even when absent in the input. misspheno1: First active phenotype missing (Y/N)? Always 'Y' if no phenotypes are loaded. missphenos: A Y/N column for each loaded phenotype. (Can be combined with misspheno1 to force at least one such column.) nmissdosage: Number of missing dosages. nmiss: Number of missing hardcalls, not counting het haploids. nmisshh: Number of missing hardcalls, counting het haploids. hethap: Number of heterozygous haploid hardcalls. nobs: Denominator (male count on chrY, otherwise total sample count). fmissdosage: Missing dosage rate. fmiss: Missing hardcall rate, not counting het haploids. fmisshh: Missing hardcall rate, counting het haploids. The default is maybefid,maybesid,missphenos,nmiss,nobs,fmiss. Supported column sets in the variant-based report are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. nmissdosage: Number of missing dosages. nmiss: Number of missing hardcalls, not counting het haploids. nmisshh: Number of missing hardcalls, counting het haploids. hethap: Number of heterozygous haploid calls. nobs: Number of potentially valid calls. fmissdosage: Missing dosage rate. fmiss: Missing hardcall rate, not counting het haploids. fmisshh: Missing hardcall rate, counting het haploids. fhethap: Heterozygous haploid rate. The default is chrom,nmiss,nobs,fmiss." argument="--missing">
|
|
|
3629 <option value="no_set" selected="True">Don't set</option>
|
|
|
3630 <option value="set">Set value(s)</option>
|
|
|
3631 </param>
|
|
|
3632 <when value="no_set">
|
|
|
3633 </when>
|
|
|
3634 <when value="set">
|
|
|
3635
|
|
|
3636 <param name="missing_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
3637 <conditional name="CONDITIONAL_missing_MOD_1">
|
|
|
3638 <param name="CONDITIONAL_SELECT_missing_MOD_1" type="select" label="How to set Missing">
|
|
|
3639 <option value="no_set" selected="True">Don't set</option>
|
|
|
3640 <option value="from_list">Select from list</option>
|
|
|
3641
|
|
|
3642 </param>
|
|
|
3643 <when value="no_set">
|
|
|
3644 </when>
|
|
|
3645
|
|
|
3646 <when value="from_list">
|
|
|
3647 <param name="missing_MOD_1" type="select" label="Select value">
|
|
1
|
3648 <option value="{sample-only"><![CDATA[{sample-only]]></option>
|
|
|
3649 <option value="variant-only}"><![CDATA[variant-only}]]></option>
|
|
0
|
3650 </param>
|
|
|
3651 </when>
|
|
|
3652 </conditional>
|
|
|
3653 <param name="missing_MOD_2_0" type="text" label="'scols='<column set descriptor>" value="" optional="False" argument="'scols='<column set descriptor>" help=""/>
|
|
|
3654 <param name="missing_MOD_3_0" type="text" label="'vcols='<column set descriptor>" value="" optional="False" argument="'vcols='<column set descriptor>" help=""/>
|
|
|
3655 </when>
|
|
|
3656 </conditional>
|
|
|
3657 <conditional name="CONDITIONAL_hardy">
|
|
|
3658 <param name="CONDITIONAL_SELECT_hardy" type="select" label="Set Hardy" help="Hardy-Weinberg exact test p-value report(s). * By default, only founders are considered; change this with --nonfounders. * chrX is now omitted from the main <output prefix>.hardy report. Instead, (if present) it gets its own <output prefix>.hardy.x report based on the method described in Graffelman J, Weir BS (2016) Hardy-Weinberg equilibrium and the X chromosome. * For variants with k alleles where k>2, k separate 'biallelic' tests are performed, each reported on its own line. However, biallelic variants are normally reported on a single line, since the counts/frequencies would be mirror-images and the p-values would be the same. You can add the 'redundant' modifier to force biallelic variant results to be reported on two lines for parsing convenience. * There is currently no special handling of case/control phenotypes. Supported column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. (A1 is always present, and positioned here.) ax: Non-A1 allele(s), comma-separated. gcounts: Hom-A1 count, total number of het-A1 calls, and total number of nonmissing calls with no copies of A1. On chrX, these are followed by male A1 and male non-A1 counts. gcount1col: gcounts values in a single comma-separated column. hetfreq: Observed and expected het-A1 frequencies. sexaf: Female and male A1 observed allele frequencies (chrX only). femalep: Female-only p/midp-value (chrX only). p: Hardy-Weinberg equilibrium exact test p/midp-value. The default is chrom,ax,gcounts,hetfreq,sexaf,p." argument="--hardy">
|
|
|
3659 <option value="no_set" selected="True">Don't set</option>
|
|
|
3660 <option value="set">Set value(s)</option>
|
|
|
3661 </param>
|
|
|
3662 <when value="no_set">
|
|
|
3663 </when>
|
|
|
3664 <when value="set">
|
|
|
3665
|
|
|
3666 <param name="hardy_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
3667 <param name="hardy_MOD_1_0" type="text" label="'midp'" value="" optional="False" argument="'midp'" help=""/>
|
|
|
3668 <param name="hardy_MOD_2_0" type="text" label="'redundant'" value="" optional="False" argument="'redundant'" help=""/>
|
|
|
3669 <param name="hardy_MOD_3_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/>
|
|
|
3670 </when>
|
|
|
3671 </conditional>
|
|
|
3672 <conditional name="CONDITIONAL_indep_pairwise">
|
|
|
3673 <param name="CONDITIONAL_SELECT_indep_pairwise" type="select" label="Set Indep pairwise" help="Generate a list of variants in approximate linkage equilibrium. * For multiallelic variants, major allele counts are used in the r^2 computation. * With the 'kb' modifier, the window size is in kilobase instead of variant count units. (Pre-'kb' space is optional, i.e. "--indep-pairwise 500 kb 0.5" and "--indep-pairwise 500kb 0.5" have the same effect.) * The step size now defaults to 1 if it's unspecified, and *must* be 1 if the window is in kilobase units. * Note that you need to rerun PLINK using --extract or --exclude on the .prune.in/.prune.out file to apply the list to another computation... and as with other applications of --extract/--exclude, duplicate variant IDs are a problem. --indep-pairwise still runs to completion for now when duplicate variant IDs are present, but that will become an error in alpha 3." argument="--indep-pairwise">
|
|
|
3674 <option value="no_set" selected="True">Don't set</option>
|
|
|
3675 <option value="set">Set value(s)</option>
|
|
|
3676 </param>
|
|
|
3677 <when value="no_set">
|
|
|
3678 </when>
|
|
|
3679 <when value="set">
|
|
|
3680
|
|
|
3681 <param name="indep_pairwise_MOD_0_0" type="text" label="window size" value="" optional="True" argument="window size" help=""/>
|
|
|
3682 <param name="indep_pairwise_MOD_1_0" type="text" label="'kb'" value="" optional="False" argument="'kb'" help=""/>
|
|
|
3683 <param name="indep_pairwise_MOD_2_0" type="text" label="step size (variant ct)" value="" optional="False" argument="step size (variant ct)" help=""/>
|
|
|
3684 <param name="indep_pairwise_MOD_3_0" type="text" label="unphased-hardcall-r^2 threshold" value="" optional="True" argument="unphased-hardcall-r^2 threshold" help=""/>
|
|
|
3685 </when>
|
|
|
3686 </conditional>
|
|
|
3687 <conditional name="CONDITIONAL_ld">
|
|
|
3688 <param name="CONDITIONAL_SELECT_ld" type="select" label="Set Ld" help="This displays diplotype frequencies, r^2, and D' for a single pair of variants. * For multiallelic variants, major allele counts/dosages are used. * Phase information is used when both variants are on the same chromosome. * When there is at least one sample with unphased het calls for both variants, diplotype frequencies are estimated using the Hill equation. If there are multiple biologically possible local maxima, all are displayed, along with HWE exact test statistics. * By default, only hardcalls are considered. Add the 'dosage' modifier if you want dosages to be taken into account. (In the diploid case, an unphased dosage of x is interpreted as P(0/0) = 1 - x, P(0/1) = x when x is in 0..1.)" argument="--ld">
|
|
|
3689 <option value="no_set" selected="True">Don't set</option>
|
|
|
3690 <option value="set">Set value(s)</option>
|
|
|
3691 </param>
|
|
|
3692 <when value="no_set">
|
|
|
3693 </when>
|
|
|
3694 <when value="set">
|
|
|
3695
|
|
|
3696 <param name="ld_MOD_0_0" type="text" label="variant ID" value="" optional="True" argument="variant ID" help=""/>
|
|
|
3697 <param name="ld_MOD_1_0" type="text" label="variant ID" value="" optional="True" argument="variant ID" help=""/>
|
|
|
3698 <param name="ld_MOD_2_0" type="text" label="'dosage'" value="" optional="False" argument="'dosage'" help=""/>
|
|
|
3699 <param name="ld_MOD_3_0" type="text" label="'hwe-midp'" value="" optional="False" argument="'hwe-midp'" help=""/>
|
|
|
3700 </when>
|
|
|
3701 </conditional>
|
|
|
3702 <conditional name="CONDITIONAL_OVERLOADED_sample_diff">
|
|
|
3703 <param name="CONDITIONAL_OVERLOADED_SELECT_sample_diff" type="select" label="Choose argument form for Sample_diff" help="Overloaded argument, must chose a form">
|
|
|
3704 <option value="form_0">Form 0</option>
|
|
|
3705 <option value="form_1">Form 1</option>
|
|
|
3706 </param>
|
|
|
3707 <when value="form_0">
|
|
|
3708
|
|
|
3709 <conditional name="CONDITIONAL_sample_diff">
|
|
|
3710 <param name="CONDITIONAL_SELECT_sample_diff" type="select" label="Set Sample diff" help="" argument="--sample-diff">
|
|
|
3711 <option value="no_set" selected="True">Don't set</option>
|
|
|
3712 <option value="set">Set value(s)</option>
|
|
|
3713 </param>
|
|
|
3714 <when value="no_set">
|
|
|
3715 </when>
|
|
|
3716 <when value="set">
|
|
|
3717
|
|
|
3718 <param name="sample_diff_MOD_0_0" type="text" label="'id-delim='<char>" value="" optional="False" argument="'id-delim='<char>" help=""/>
|
|
|
3719 <conditional name="CONDITIONAL_sample_diff_MOD_1">
|
|
|
3720 <param name="CONDITIONAL_SELECT_sample_diff_MOD_1" type="select" label="How to set Sample diff">
|
|
|
3721 <option value="no_set" selected="True">Don't set</option>
|
|
|
3722 <option value="from_list">Select from list</option>
|
|
|
3723
|
|
|
3724 </param>
|
|
|
3725 <when value="no_set">
|
|
|
3726 </when>
|
|
|
3727
|
|
|
3728 <when value="from_list">
|
|
|
3729 <param name="sample_diff_MOD_1" type="select" label="Select value">
|
|
1
|
3730 <option value="'dosage'"><![CDATA['dosage']]></option>
|
|
|
3731 <option value="'dosage='<tolerance>"><![CDATA['dosage='<tolerance>]]></option>
|
|
0
|
3732 </param>
|
|
|
3733 </when>
|
|
|
3734 </conditional>
|
|
|
3735 <param name="sample_diff_MOD_2_0" type="text" label="'include-missing'" value="" optional="False" argument="'include-missing'" help=""/>
|
|
|
3736 <conditional name="CONDITIONAL_sample_diff_MOD_3">
|
|
|
3737 <param name="CONDITIONAL_SELECT_sample_diff_MOD_3" type="select" label="How to set Sample diff">
|
|
|
3738 <option value="no_set" selected="True">Don't set</option>
|
|
|
3739 <option value="from_list">Select from list</option>
|
|
|
3740
|
|
|
3741 </param>
|
|
|
3742 <when value="no_set">
|
|
|
3743 </when>
|
|
|
3744
|
|
|
3745 <when value="from_list">
|
|
|
3746 <param name="sample_diff_MOD_3" type="select" label="Select value">
|
|
1
|
3747 <option value="{pairwise"><![CDATA[{pairwise]]></option>
|
|
|
3748 <option value="counts-only}"><![CDATA[counts-only}]]></option>
|
|
0
|
3749 </param>
|
|
|
3750 </when>
|
|
|
3751 </conditional>
|
|
|
3752 <param name="sample_diff_MOD_4_0" type="text" label="'fname-id-delim='<c>" value="" optional="False" argument="'fname-id-delim='<c>" help=""/>
|
|
|
3753 <param name="sample_diff_MOD_5_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
3754 <param name="sample_diff_MOD_6_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/>
|
|
|
3755 <param name="sample_diff_MOD_7_0" type="text" label="'counts-cols='<column set descriptor>" value="" optional="False" argument="'counts-cols='<column set descriptor>" help=""/>
|
|
|
3756 <conditional name="CONDITIONAL_sample_diff_MOD_8">
|
|
|
3757 <param name="CONDITIONAL_SELECT_sample_diff_MOD_8" type="select" label="How to set Sample diff">
|
|
|
3758 <option value="no_set" selected="True">Don't set</option>
|
|
|
3759 <option value="from_list">Select from list</option>
|
|
|
3760
|
|
|
3761 </param>
|
|
|
3762 <when value="no_set">
|
|
|
3763 </when>
|
|
|
3764
|
|
|
3765 <when value="from_list">
|
|
|
3766 <param name="sample_diff_MOD_8" type="select" label="Select value">
|
|
1
|
3767 <option value="base="><![CDATA[base=]]></option>
|
|
|
3768 <option value="ids="><![CDATA[ids=]]></option>
|
|
0
|
3769 </param>
|
|
|
3770 </when>
|
|
|
3771 </conditional>
|
|
|
3772 <param name="sample_diff_MOD_9_0" type="text" label="sample ID" value="" optional="True" argument="sample ID" help=""/>
|
|
|
3773 <param name="sample_diff_MOD_10_0" type="text" label="other sample ID(s)..." value="" optional="False" argument="other sample ID(s)..." help="Multiple values are allowed"/>
|
|
|
3774 </when>
|
|
|
3775 </conditional>
|
|
|
3776 </when>
|
|
|
3777 <when value="form_1">
|
|
|
3778
|
|
|
3779 <conditional name="CONDITIONAL_sample_diff">
|
|
|
3780 <param name="CONDITIONAL_SELECT_sample_diff" type="select" label="Set Sample diff" help="(alias: --sdiff) Report discordances and discordance-counts between pairs of samples. If chrX or chrY is present, sex must be defined and consistent. * There are three ways to specify which sample pairs to compare. To compare a single baseline sample against some others, start the (space-delimited) sample ID list with 'base='. To perform an all-vs.-all comparison, start it with 'ids=' instead. To compare sample pairs listed in a file, use 'file='. Note that 'base='/'ids='/'file=' must be positioned after all modifiers. * Sample IDs are interpreted as if they were in a VCF header line, with 'id-delim=' having the usual effect. * By default, comparisons are based on hardcalls. Use 'dosage' to compare dosages instead; you can combine this with a tolerance in [0, 0.5). * By default, if one genotype is missing and the other isn't, that doesn't count as a difference; this can be changed with 'include-missing'. * By default, a single main report is written to <output prefix>[.<base ID>].sdiff. To write separate pairwise <output prefix>.<ID1>.<ID2>.sdiff reports for each compared ID pair, add the 'pairwise' modifier. To omit the main report, add the 'counts-only' modifier. (Note that, if you're only interested in nonmissing autosomal biallelic hardcalls, --make-king-table provides a more efficient way to compute just counts.) * By default, if an output filename has a multipart sample ID, the parts will be delimited by '_'; use 'fname-id-delim=' to change this. Supported main-report column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (Variant ID is always present, and positioned here.) ref: Reference allele. alt: All alternate alleles, comma-separated. maybefid: FID1/FID2, if that column was in the input. Requires 'id'. fid: Force FID1/FID2 even when FID was absent in the input. id: IID1/IID2. maybesid: SID1/SID2, if that column was in the input. Requires 'id'. sid: Force SID1/SID2 even when SID was absent in the input. geno: Unphased GT or DS for the two samples. The default is usually chrom,pos,ref,alt,maybefid,id,maybesid,geno; the sample IDs are removed from the default in 'pairwise' mode. Supported discordance-count-summary column sets are: maybefid: FID1/FID2, if that column was in the input. fid: Force FID1/FID2 even when FID was absent in the input. (IID1/IID2 are always present.) maybesid: SID1/SID2, if that column was in the input. sid: Force SID1/SID2 even when SID was absent in the input. nobs: Number of variants considered. This includes variants where one or both variants are missing iff 'include-missing' was specified. nobsibs: ibs0+ibs1+ibs2. ibs0: Number of diploid variants with no common hardcall alleles. ibs1: Number of diploid variants with exactly 1 common hardcall allele. ibs2: Number of diploid variants with both hardcall alleles matching. halfmiss: Number of variants with exactly 1 missing genotype/dosage. Ignored without 'include-missing'. diff: Total number of differences. The default is maybefid,maybesid,nobs,halfmiss,diff." argument="--sample-diff">
|
|
|
3781 <option value="no_set" selected="True">Don't set</option>
|
|
|
3782 <option value="set">Set value(s)</option>
|
|
|
3783 </param>
|
|
|
3784 <when value="no_set">
|
|
|
3785 </when>
|
|
|
3786 <when value="set">
|
|
|
3787
|
|
|
3788 <param name="sample_diff_MOD_0_0" type="text" label="'id-delim='<char>" value="" optional="False" argument="'id-delim='<char>" help=""/>
|
|
|
3789 <conditional name="CONDITIONAL_sample_diff_MOD_1">
|
|
|
3790 <param name="CONDITIONAL_SELECT_sample_diff_MOD_1" type="select" label="How to set Sample diff">
|
|
|
3791 <option value="no_set" selected="True">Don't set</option>
|
|
|
3792 <option value="from_list">Select from list</option>
|
|
|
3793
|
|
|
3794 </param>
|
|
|
3795 <when value="no_set">
|
|
|
3796 </when>
|
|
|
3797
|
|
|
3798 <when value="from_list">
|
|
|
3799 <param name="sample_diff_MOD_1" type="select" label="Select value">
|
|
1
|
3800 <option value="'dosage'"><![CDATA['dosage']]></option>
|
|
|
3801 <option value="'dosage='<tolerance>"><![CDATA['dosage='<tolerance>]]></option>
|
|
0
|
3802 </param>
|
|
|
3803 </when>
|
|
|
3804 </conditional>
|
|
|
3805 <param name="sample_diff_MOD_2_0" type="text" label="'include-missing'" value="" optional="False" argument="'include-missing'" help=""/>
|
|
|
3806 <conditional name="CONDITIONAL_sample_diff_MOD_3">
|
|
|
3807 <param name="CONDITIONAL_SELECT_sample_diff_MOD_3" type="select" label="How to set Sample diff">
|
|
|
3808 <option value="no_set" selected="True">Don't set</option>
|
|
|
3809 <option value="from_list">Select from list</option>
|
|
|
3810
|
|
|
3811 </param>
|
|
|
3812 <when value="no_set">
|
|
|
3813 </when>
|
|
|
3814
|
|
|
3815 <when value="from_list">
|
|
|
3816 <param name="sample_diff_MOD_3" type="select" label="Select value">
|
|
1
|
3817 <option value="{pairwise"><![CDATA[{pairwise]]></option>
|
|
|
3818 <option value="counts-only}"><![CDATA[counts-only}]]></option>
|
|
0
|
3819 </param>
|
|
|
3820 </when>
|
|
|
3821 </conditional>
|
|
|
3822 <param name="sample_diff_MOD_4_0" type="text" label="'fname-id-delim='<c>" value="" optional="False" argument="'fname-id-delim='<c>" help=""/>
|
|
|
3823 <param name="sample_diff_MOD_5_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
3824 <param name="sample_diff_MOD_6_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/>
|
|
|
3825 <param name="sample_diff_MOD_7_0" type="text" label="'counts-cols='<column set descriptor>" value="" optional="False" argument="'counts-cols='<column set descriptor>" help=""/>
|
|
|
3826 <param name="sample_diff_MOD_8_0" type="text" label="ID-pair file" value="" optional="True" argument="ID-pair file" help=""/>
|
|
|
3827 </when>
|
|
|
3828 </conditional>
|
|
|
3829 </when>
|
|
|
3830 </conditional>
|
|
|
3831 <conditional name="CONDITIONAL_make_king">
|
|
|
3832 <param name="CONDITIONAL_SELECT_make_king" type="select" label="Set Make king" help="KING-robust kinship estimator, described by Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM (2010) Robust relationship inference in genome-wide association studies. By default, this writes a lower-triangular tab-delimited table of kinship coefficients to <output prefix>.king, and a list of the corresponding sample IDs to <output prefix>.king.id. The first row of the .king file contains a single <genome 1-genome 2> kinship coefficient, the second row has the <genome 1-genome 3> and <genome 2-genome 3> kinship values in that order, etc. * Only autosomes are currently considered. * Pedigree information is currently ignored; the between-family estimator is used for all pairs. * For multiallelic variants, REF allele counts are used. * If the 'square' or 'square0' modifier is present, a square matrix is written instead; 'square0' fills the upper right triangle with zeroes. * If the 'zs' modifier is present, the .king file is Zstd-compressed. * If the 'bin' modifier is present, a binary (square) matrix of double-precision floating point values, suitable for loading from R, is instead written to <output prefix>.king.bin. ('bin4' specifies single-precision numbers instead.) This can be combined with 'square0' if you still want the upper right zeroed out, or 'triangle' if you don't want to pad the upper right at all. * The computation can be subdivided with --parallel." argument="--make-king">
|
|
|
3833 <option value="no_set" selected="True">Don't set</option>
|
|
|
3834 <option value="set">Set value(s)</option>
|
|
|
3835 </param>
|
|
|
3836 <when value="no_set">
|
|
|
3837 </when>
|
|
|
3838 <when value="set">
|
|
|
3839
|
|
|
3840 <conditional name="CONDITIONAL_make_king_MOD_0">
|
|
|
3841 <param name="CONDITIONAL_SELECT_make_king_MOD_0" type="select" label="How to set Make king">
|
|
|
3842 <option value="no_set" selected="True">Don't set</option>
|
|
|
3843 <option value="from_list">Select from list</option>
|
|
|
3844
|
|
|
3845 </param>
|
|
|
3846 <when value="no_set">
|
|
|
3847 </when>
|
|
|
3848
|
|
|
3849 <when value="from_list">
|
|
|
3850 <param name="make_king_MOD_0" type="select" label="Select value">
|
|
1
|
3851 <option value="{square"><![CDATA[{square]]></option>
|
|
|
3852 <option value="square0"><![CDATA[square0]]></option>
|
|
|
3853 <option value="triangle}"><![CDATA[triangle}]]></option>
|
|
0
|
3854 </param>
|
|
|
3855 </when>
|
|
|
3856 </conditional>
|
|
|
3857 <conditional name="CONDITIONAL_make_king_MOD_1">
|
|
|
3858 <param name="CONDITIONAL_SELECT_make_king_MOD_1" type="select" label="How to set Make king">
|
|
|
3859 <option value="no_set" selected="True">Don't set</option>
|
|
|
3860 <option value="from_list">Select from list</option>
|
|
|
3861
|
|
|
3862 </param>
|
|
|
3863 <when value="no_set">
|
|
|
3864 </when>
|
|
|
3865
|
|
|
3866 <when value="from_list">
|
|
|
3867 <param name="make_king_MOD_1" type="select" label="Select value">
|
|
1
|
3868 <option value="{zs"><![CDATA[{zs]]></option>
|
|
|
3869 <option value="bin"><![CDATA[bin]]></option>
|
|
|
3870 <option value="bin4}"><![CDATA[bin4}]]></option>
|
|
0
|
3871 </param>
|
|
|
3872 </when>
|
|
|
3873 </conditional>
|
|
|
3874 </when>
|
|
|
3875 </conditional>
|
|
|
3876 <conditional name="CONDITIONAL_make_king_table">
|
|
|
3877 <param name="CONDITIONAL_SELECT_make_king_table" type="select" label="Set Make king table" help="Similar to --make-king, except results are reported in KING's original .kin0 text table format (with minor changes, e.g. row order is more friendly to incremental addition of samples), --king-table-filter can be used to restrict the report to high kinship values, and the 'rel-check' modifier can be used to restrict to same-FID pairs. Supported column sets are: maybefid: FID1/FID2, if that column was in the input. Requires 'id'. fid: Force FID1/FID2 even when FID was absent in the input. id: IID1/IID2 (column headers are actually 'ID1'/'ID2' to match KING). maybesid: SID1/SID2, if that column was in the input. Requires 'id'. sid: Force SID1/SID2 even when SID was absent in the input. nsnp: Number of variants considered (autosomal, neither call missing). hethet: Proportion/count of considered call pairs which are het-het. ibs0: Proportion/count of considered call pairs which are opposite homs. ibs1: HET1_HOM2 and HET2_HOM1 proportions/counts. kinship: KING-robust between-family kinship estimator. The default is maybefid,id,maybesid,nsnp,hethet,ibs0,kinship. hethet/ibs0/ibs1 values are proportions unless the 'counts' modifier is present. If id is omitted, a .kin0.id file is also written." argument="--make-king-table">
|
|
|
3878 <option value="no_set" selected="True">Don't set</option>
|
|
|
3879 <option value="set">Set value(s)</option>
|
|
|
3880 </param>
|
|
|
3881 <when value="no_set">
|
|
|
3882 </when>
|
|
|
3883 <when value="set">
|
|
|
3884
|
|
|
3885 <param name="make_king_table_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
3886 <param name="make_king_table_MOD_1_0" type="text" label="'counts'" value="" optional="False" argument="'counts'" help=""/>
|
|
|
3887 <param name="make_king_table_MOD_2_0" type="text" label="'rel-check'" value="" optional="False" argument="'rel-check'" help=""/>
|
|
|
3888 <param name="make_king_table_MOD_3_0" type="text" label="'cols='<col set descrip.>" value="" optional="False" argument="'cols='<col set descrip.>" help=""/>
|
|
|
3889 </when>
|
|
|
3890 </conditional>
|
|
|
3891 <conditional name="CONDITIONAL_make_rel">
|
|
|
3892 <param name="CONDITIONAL_SELECT_make_rel" type="select" label="Set Make rel" help="Write a lower-triangular variance-standardized relationship matrix to <output prefix>.rel, and corresponding IDs to <output prefix>.rel.id. * This computation assumes that variants do not have very low MAF, or deviate greatly from Hardy-Weinberg equilibrium. * Also, it's usually best to perform this calculation on a variant set in approximate linkage equilibrium. * The 'cov' modifier replaces the variance-standardization step with basic mean-centering, causing a covariance matrix to be calculated instead. * The computation can be subdivided with --parallel." argument="--make-rel">
|
|
|
3893 <option value="no_set" selected="True">Don't set</option>
|
|
|
3894 <option value="set">Set value(s)</option>
|
|
|
3895 </param>
|
|
|
3896 <when value="no_set">
|
|
|
3897 </when>
|
|
|
3898 <when value="set">
|
|
|
3899
|
|
|
3900 <param name="make_rel_MOD_0_0" type="text" label="'cov'" value="" optional="False" argument="'cov'" help=""/>
|
|
|
3901 <param name="make_rel_MOD_1_0" type="text" label="'meanimpute'" value="" optional="False" argument="'meanimpute'" help=""/>
|
|
|
3902 <conditional name="CONDITIONAL_make_rel_MOD_2">
|
|
|
3903 <param name="CONDITIONAL_SELECT_make_rel_MOD_2" type="select" label="How to set Make rel">
|
|
|
3904 <option value="no_set" selected="True">Don't set</option>
|
|
|
3905 <option value="from_list">Select from list</option>
|
|
|
3906
|
|
|
3907 </param>
|
|
|
3908 <when value="no_set">
|
|
|
3909 </when>
|
|
|
3910
|
|
|
3911 <when value="from_list">
|
|
|
3912 <param name="make_rel_MOD_2" type="select" label="Select value">
|
|
1
|
3913 <option value="{square"><![CDATA[{square]]></option>
|
|
|
3914 <option value="square0"><![CDATA[square0]]></option>
|
|
|
3915 <option value="triangle}"><![CDATA[triangle}]]></option>
|
|
0
|
3916 </param>
|
|
|
3917 </when>
|
|
|
3918 </conditional>
|
|
|
3919 <conditional name="CONDITIONAL_make_rel_MOD_3">
|
|
|
3920 <param name="CONDITIONAL_SELECT_make_rel_MOD_3" type="select" label="How to set Make rel">
|
|
|
3921 <option value="no_set" selected="True">Don't set</option>
|
|
|
3922 <option value="from_list">Select from list</option>
|
|
|
3923
|
|
|
3924 </param>
|
|
|
3925 <when value="no_set">
|
|
|
3926 </when>
|
|
|
3927
|
|
|
3928 <when value="from_list">
|
|
|
3929 <param name="make_rel_MOD_3" type="select" label="Select value">
|
|
1
|
3930 <option value="{zs"><![CDATA[{zs]]></option>
|
|
|
3931 <option value="bin"><![CDATA[bin]]></option>
|
|
|
3932 <option value="bin4}"><![CDATA[bin4}]]></option>
|
|
0
|
3933 </param>
|
|
|
3934 </when>
|
|
|
3935 </conditional>
|
|
|
3936 </when>
|
|
|
3937 </conditional>
|
|
|
3938 <conditional name="CONDITIONAL_make_grm_list">
|
|
|
3939 <param name="CONDITIONAL_SELECT_make_grm_list" type="select" label="Set Make grm list" help="" argument="--make-grm-list">
|
|
|
3940 <option value="no_set" selected="True">Don't set</option>
|
|
|
3941 <option value="set">Set value(s)</option>
|
|
|
3942 </param>
|
|
|
3943 <when value="no_set">
|
|
|
3944 </when>
|
|
|
3945 <when value="set">
|
|
|
3946
|
|
|
3947 <param name="make_grm_list_MOD_0_0" type="text" label="'cov'" value="" optional="False" argument="'cov'" help=""/>
|
|
|
3948 <param name="make_grm_list_MOD_1_0" type="text" label="'meanimpute'" value="" optional="False" argument="'meanimpute'" help=""/>
|
|
|
3949 <param name="make_grm_list_MOD_2_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
3950 <conditional name="CONDITIONAL_make_grm_list_MOD_3">
|
|
|
3951 <param name="CONDITIONAL_SELECT_make_grm_list_MOD_3" type="select" label="How to set Make grm list">
|
|
|
3952 <option value="no_set" selected="True">Don't set</option>
|
|
|
3953 <option value="from_list">Select from list</option>
|
|
|
3954
|
|
|
3955 </param>
|
|
|
3956 <when value="no_set">
|
|
|
3957 </when>
|
|
|
3958
|
|
|
3959 <when value="from_list">
|
|
|
3960 <param name="make_grm_list_MOD_3" type="select" label="Select value">
|
|
1
|
3961 <option value="{id-header"><![CDATA[{id-header]]></option>
|
|
|
3962 <option value="iid-only}"><![CDATA[iid-only}]]></option>
|
|
0
|
3963 </param>
|
|
|
3964 </when>
|
|
|
3965 </conditional>
|
|
|
3966 </when>
|
|
|
3967 </conditional>
|
|
|
3968 <conditional name="CONDITIONAL_make_grm_bin">
|
|
|
3969 <param name="CONDITIONAL_SELECT_make_grm_bin" type="select" label="Set Make grm bin" help="--make-grm-list causes the relationships to be written to GCTA's original list format, which describes one pair per line, while --make-grm-bin writes them in GCTA 1.1+'s single-precision triangular binary format. Note that these formats explicitly report the number of valid observations (where neither sample has a missing call) for each pair, which is useful input for some scripts." argument="--make-grm-bin">
|
|
|
3970 <option value="no_set" selected="True">Don't set</option>
|
|
|
3971 <option value="set">Set value(s)</option>
|
|
|
3972 </param>
|
|
|
3973 <when value="no_set">
|
|
|
3974 </when>
|
|
|
3975 <when value="set">
|
|
|
3976
|
|
|
3977 <param name="make_grm_bin_MOD_0_0" type="text" label="'cov'" value="" optional="False" argument="'cov'" help=""/>
|
|
|
3978 <param name="make_grm_bin_MOD_1_0" type="text" label="'meanimpute'" value="" optional="False" argument="'meanimpute'" help=""/>
|
|
|
3979 <conditional name="CONDITIONAL_make_grm_bin_MOD_2">
|
|
|
3980 <param name="CONDITIONAL_SELECT_make_grm_bin_MOD_2" type="select" label="How to set Make grm bin">
|
|
|
3981 <option value="no_set" selected="True">Don't set</option>
|
|
|
3982 <option value="from_list">Select from list</option>
|
|
|
3983
|
|
|
3984 </param>
|
|
|
3985 <when value="no_set">
|
|
|
3986 </when>
|
|
|
3987
|
|
|
3988 <when value="from_list">
|
|
|
3989 <param name="make_grm_bin_MOD_2" type="select" label="Select value">
|
|
1
|
3990 <option value="{id-header"><![CDATA[{id-header]]></option>
|
|
|
3991 <option value="iid-only}"><![CDATA[iid-only}]]></option>
|
|
0
|
3992 </param>
|
|
|
3993 </when>
|
|
|
3994 </conditional>
|
|
|
3995 </when>
|
|
|
3996 </conditional>
|
|
|
3997 <conditional name="CONDITIONAL_OVERLOADED_pca">
|
|
|
3998 <param name="CONDITIONAL_OVERLOADED_SELECT_pca" type="select" label="Choose argument form for Pca" help="Overloaded argument, must chose a form">
|
|
|
3999 <option value="form_0">Form 0</option>
|
|
|
4000 <option value="form_1">Form 1</option>
|
|
|
4001 </param>
|
|
|
4002 <when value="form_0">
|
|
|
4003
|
|
|
4004 <conditional name="CONDITIONAL_pca">
|
|
|
4005 <param name="CONDITIONAL_SELECT_pca" type="select" label="Set Pca" help="" argument="--pca">
|
|
|
4006 <option value="no_set" selected="True">Don't set</option>
|
|
|
4007 <option value="set">Set value(s)</option>
|
|
|
4008 </param>
|
|
|
4009 <when value="no_set">
|
|
|
4010 </when>
|
|
|
4011 <when value="set">
|
|
|
4012
|
|
|
4013 <param name="pca_MOD_0_0" type="text" label="count" value="" optional="False" argument="count" help=""/>
|
|
|
4014 <conditional name="CONDITIONAL_pca_MOD_1">
|
|
|
4015 <param name="CONDITIONAL_SELECT_pca_MOD_1" type="select" label="How to set Pca">
|
|
|
4016 <option value="no_set" selected="True">Don't set</option>
|
|
|
4017 <option value="from_list">Select from list</option>
|
|
|
4018
|
|
|
4019 </param>
|
|
|
4020 <when value="no_set">
|
|
|
4021 </when>
|
|
|
4022
|
|
|
4023 <when value="from_list">
|
|
|
4024 <param name="pca_MOD_1" type="select" label="Select value">
|
|
1
|
4025 <option value="{approx"><![CDATA[{approx]]></option>
|
|
|
4026 <option value="meanimpute}"><![CDATA[meanimpute}]]></option>
|
|
0
|
4027 </param>
|
|
|
4028 </when>
|
|
|
4029 </conditional>
|
|
|
4030 <param name="pca_MOD_2_0" type="text" label="'scols='<col set descriptor>" value="" optional="False" argument="'scols='<col set descriptor>" help=""/>
|
|
|
4031 </when>
|
|
|
4032 </conditional>
|
|
|
4033 </when>
|
|
|
4034 <when value="form_1">
|
|
|
4035
|
|
|
4036 <conditional name="CONDITIONAL_pca">
|
|
|
4037 <param name="CONDITIONAL_SELECT_pca" type="select" label="Set Pca" help="['scols='<col set descriptor>] ['vcols='<col set descriptor>] Extracts top principal components from the variance-standardized relationship matrix. * It is usually best to perform this calculation on a variant set in approximate linkage equilibrium, with no very-low-MAF variants. * By default, 10 PCs are extracted; you can adjust this by passing a numeric parameter. (Note that 10 is lower than the PLINK 1.9 default of 20; this is due to the randomized algorithm's memory footprint growing quadratically w.r.t. the PC count.) * The 'approx' modifier causes the standard deterministic computation to be replaced with the randomized algorithm originally implemented for Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ, Price AL (2016) Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia. This can be a good idea when you have >5k samples. * The randomized algorithm always uses mean imputation for missing genotype calls. For comparison purposes, you can use the 'meanimpute' modifier to request this behavior for the standard computation. * 'scols=' can be used to customize how sample IDs appear in the .eigenvec file. (maybefid, fid, maybesid, and sid supported; default is maybefid,maybesid.) * The 'biallelic-var-wts' modifier requests an additional one-line-per-variant .eigenvec.var file with PCs expressed as variant weights instead of sample weights, with the condition that all variants must be biallelic. When it's present, 'vzs' causes the .eigenvec.var file to be Zstd-compressed. 'vcols=' can be used to customize the report columns; supported column sets are: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. maj: Major allele. nonmaj: All nonmajor alleles, comma-separated. (PCs are always present, and positioned here. Signs are w.r.t. the major, not necessarily reference, allele.) Default is chrom,maj,nonmaj. * In this build, 'var-wts' generates the same report as biallelic-var-wts, except with the "all variants must be biallelic" restriction lifted. This is temporary. It will no longer be supported as of alpha 3; instead, there will be an 'allele-wts' mode which seamlessly handles multiallelic variants, at the cost of generating more verbose one-line-per-allele output." argument="--pca">
|
|
|
4038 <option value="no_set" selected="True">Don't set</option>
|
|
|
4039 <option value="set">Set value(s)</option>
|
|
|
4040 </param>
|
|
|
4041 <when value="no_set">
|
|
|
4042 </when>
|
|
|
4043 <when value="set">
|
|
|
4044
|
|
|
4045 <conditional name="CONDITIONAL_pca_MOD_0">
|
|
|
4046 <param name="CONDITIONAL_SELECT_pca_MOD_0" type="select" label="How to set Pca">
|
|
|
4047 <option value="no_set" selected="True">Don't set</option>
|
|
|
4048 <option value="from_list">Select from list</option>
|
|
|
4049
|
|
|
4050 </param>
|
|
|
4051 <when value="no_set">
|
|
|
4052 </when>
|
|
|
4053
|
|
|
4054 <when value="from_list">
|
|
|
4055 <param name="pca_MOD_0" type="select" label="Select value">
|
|
1
|
4056 <option value="{biallelic-var-wts"><![CDATA[{biallelic-var-wts]]></option>
|
|
|
4057 <option value="var-wts}"><![CDATA[var-wts}]]></option>
|
|
0
|
4058 </param>
|
|
|
4059 </when>
|
|
|
4060 </conditional>
|
|
|
4061 <param name="pca_MOD_1_0" type="text" label="count" value="" optional="False" argument="count" help=""/>
|
|
|
4062 <conditional name="CONDITIONAL_pca_MOD_2">
|
|
|
4063 <param name="CONDITIONAL_SELECT_pca_MOD_2" type="select" label="How to set Pca">
|
|
|
4064 <option value="no_set" selected="True">Don't set</option>
|
|
|
4065 <option value="from_list">Select from list</option>
|
|
|
4066
|
|
|
4067 </param>
|
|
|
4068 <when value="no_set">
|
|
|
4069 </when>
|
|
|
4070
|
|
|
4071 <when value="from_list">
|
|
|
4072 <param name="pca_MOD_2" type="select" label="Select value">
|
|
1
|
4073 <option value="{approx"><![CDATA[{approx]]></option>
|
|
|
4074 <option value="meanimpute}"><![CDATA[meanimpute}]]></option>
|
|
0
|
4075 </param>
|
|
|
4076 </when>
|
|
|
4077 </conditional>
|
|
|
4078 <param name="pca_MOD_3_0" type="text" label="'vzs'" value="" optional="False" argument="'vzs'" help=""/>
|
|
|
4079 </when>
|
|
|
4080 </conditional>
|
|
|
4081 </when>
|
|
|
4082 </conditional>
|
|
|
4083 <conditional name="CONDITIONAL_king_cutoff">
|
|
|
4084 <param name="CONDITIONAL_SELECT_king_cutoff" type="select" label="Set King cutoff" help="Exclude one member of each pair of samples with KING-robust kinship greater than the given threshold. Remaining/excluded sample IDs are written to <output prefix>.king.cutoff.in.id + .king.cutoff.out.id. If present, the .king.bin file must be triangular (either precision is ok)." argument="--king-cutoff">
|
|
|
4085 <option value="no_set" selected="True">Don't set</option>
|
|
|
4086 <option value="set">Set value(s)</option>
|
|
|
4087 </param>
|
|
|
4088 <when value="no_set">
|
|
|
4089 </when>
|
|
|
4090 <when value="set">
|
|
|
4091
|
|
|
4092 <param name="king_cutoff_MOD_0_0" type="text" label=".king.bin + .king.id fileset prefix" value="" optional="False" argument=".king.bin + .king.id fileset prefix" help=""/>
|
|
|
4093 <param name="king_cutoff_MOD_1_0" type="text" label="threshold" value="" optional="True" argument="threshold" help=""/>
|
|
|
4094 </when>
|
|
|
4095 </conditional>
|
|
|
4096 <conditional name="CONDITIONAL_write_covar">
|
|
|
4097 <param name="CONDITIONAL_SELECT_write_covar" type="select" label="Set Write covar" help="If covariates are defined, an updated version (with all filters applied) is automatically written to <output prefix>.cov whenever --make-pgen, --make-just-psam, --export, or a similar command is present. However, if you do not wish to simultaneously generate a new sample file, you can use --write-covar to just produce a pruned covariate file. Supported column sets are: maybefid: FID, if that column was in the input. fid: Force FID column to be written even when absent in the input. maybesid: SID, if that column was in the input. sid: Force SID column to be written even when absent in the input. maybeparents: Father/mother IIDs ('0' = missing), if columns in input. parents: Force PAT/MAT columns to be written even when absent in input. sex: '1' = male, '2' = female, 'NA' = missing. pheno1: First active phenotype. If none, all column entries are set to the --output-missing-phenotype string. phenos: All active phenotypes, if any. (Can be combined with pheno1 to force at least one phenotype column to be written.) (Covariates are always present, and positioned here.) The default is maybefid,maybesid." argument="--write-covar">
|
|
|
4098 <option value="no_set" selected="True">Don't set</option>
|
|
|
4099 <option value="set">Set value(s)</option>
|
|
|
4100 </param>
|
|
|
4101 <when value="no_set">
|
|
|
4102 </when>
|
|
|
4103 <when value="set">
|
|
|
4104
|
|
|
4105 <param name="write_covar_MOD_0_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/>
|
|
|
4106 </when>
|
|
|
4107 </conditional>
|
|
|
4108 <param name="write_samples" type="boolean" label="Write samples" truevalue="--write-samples" falsevalue="" optional="true" argument="--write-samples" help="Report IDs of all samples which pass your filters/inclusion thresholds." checked="False"/>
|
|
|
4109 <conditional name="CONDITIONAL_write_snplist">
|
|
|
4110 <param name="CONDITIONAL_SELECT_write_snplist" type="select" label="Set Write snplist" help="List all variants which pass your filters/inclusion thresholds." argument="--write-snplist">
|
|
|
4111 <option value="no_set" selected="True">Don't set</option>
|
|
|
4112 <option value="set">Set value(s)</option>
|
|
|
4113 </param>
|
|
|
4114 <when value="no_set">
|
|
|
4115 </when>
|
|
|
4116 <when value="set">
|
|
|
4117
|
|
|
4118 <param name="write_snplist_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
4119 </when>
|
|
|
4120 </conditional>
|
|
|
4121 <conditional name="CONDITIONAL_glm">
|
|
|
4122 <param name="CONDITIONAL_SELECT_glm" type="select" label="Set Glm" help="[{genotypic | hethom | dominant | recessive}] ['interaction'] ['hide-covar'] ['intercept'] [{no-firth | firth-fallback | firth}] ['cols='<col set desc.>] ['local-covar='<file>] ['local-pvar='<file>] ['local-psam='<file>] ['local-omit-last' | 'local-cats='<category ct>] Basic association analysis on quantitative and/or case/control phenotypes. For each variant, a linear (for quantitative traits) or logistic (for case/control) regression is run with the phenotype as the dependent variable, and nonmajor allele dosage(s) and a constant-1 column as predictors. * There is usually an additive effect line for every nonmajor allele, and no such line for the major allele. To omit REF alleles instead of major alleles, add the 'omit-ref' modifier. (When performing interaction testing, this tends to cause the multicollinearity check to fail for low-ref-frequency variants.) * By default, sex (male = 1, female = 2; note that this is a change from PLINK 1.x) is automatically added as a predictor for X chromosome variants, and no others. The 'sex' modifier causes it to be added everywhere (except chrY), while 'no-x-sex' excludes it entirely. * The 'log10' modifier causes p-values to be reported in -log10(p) form. * 'pheno-ids' causes the samples used in each set of regressions to be written to an .id file. (When the samples differ on chrX or chrY, .x.id and/or .y.id files are also written.) * The 'genotypic' modifier adds an additive effect/dominance deviation 2df joint test (0-2 and 0..1..0 coding), while 'hethom' uses 0..0..1 and 0..1..0 coding instead. * 'dominant' and 'recessive' specify a model assuming full dominance or recessiveness, respectively, for the ref allele. I.e. the genotype column is recoded as 0..1..1 or 0..0..1, respectively. * 'interaction' adds genotype x covariate interactions to the model. Note that this tends to produce 'NA' results (due to the multicollinearity check) when the reference allele is 'wrong'; --maj-ref can be used to enable analysis of those variants. * Additional predictors can be added with --covar. By default, association statistics are reported for all nonconstant predictors; 'hide-covar' suppresses covariate-only results, while 'intercept' causes intercepts to be reported. * For logistic regression, when the phenotype [quasi-]separates the genotype, an NA result is currently reported by default. To fall back on Firth logistic regression instead when the basic logistic regression fails to converge, add the 'firth-fallback' modifier (highly recommended, will become the default when beta testing begins). To eliminate the special case and use Firth logistic regression everywhere, add 'firth'. 'no-firth' can be used to prevent Firth regression from being attempted in a way that'll still work after alpha testing completes. * To add covariates which are not constant across all variants, add the 'local-covar=', 'local-pvar=', and 'local-psam=' modifiers, and use full filenames for each. Normally, the local-covar file should have c * n real-valued columns, where the first c columns correspond to the first sample in the local-psam file, columns (c+1) to 2c correspond to the second sample, etc.; and the mth line corresponds to the mth nonheader line of the local-pvar file. (Variants outside of the local-pvar file are excluded from the regression.) The local covariates are assigned the names LOCAL1, LOCAL2, etc.; to exclude the last local covariate from the regression (necessary if they are e.g. local ancestry coefficients which sum to 1), add 'local-omit-last'. Alternatively, with 'local-cats='<k>, the local-covar file is expected to have n columns with integer-valued entries in [1, k]. These category assignments are expanded into (k-1) local covariates in the usual manner. The main report supports the following column sets: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. (A1 is always present, and positioned here. For multiallelic variants, this column may contain multiple comma-separated alleles when the result doesn't depend on which allele is A1.) ax: Non-A1 alleles, comma-separated. a1count: A1 allele count (can be decimal with dosage data). totallele: Allele observation count (can be higher than --freq value, due to inclusion of het haploids and chrX model). a1countcc: A1 count in cases, then controls (case/control only). totallelecc: Case and control allele observation counts. gcountcc: Genotype hardcall counts (neither-A1, het-A1, A1-A1) in cases, then controls (case/control only). a1freq: A1 allele frequency. a1freqcc: A1 frequency in cases, then controls (case/control only). machr2: Unphased MaCH imputation quality (frequently labeled 'INFO'). firth: Reports whether Firth regression was used (firth-fallback only). test: Test identifier. (Required unless only one test is run.) nobs: Number of samples in the regression. beta: Regression coefficient (for A1 if additive test). orbeta: Odds ratio for case/control, beta for quantitative traits. (Ignored if 'beta' column set included.) se: Standard error of beta. ci: Bounds of symmetric approximate confidence interval (requires --ci). tz: T-statistic for linear regression, Wald Z-score for logistic/Firth. p: Asymptotic p-value (or -log10(p)) for T/Z-statistic. err: Error code for NA results. The default is chrom,pos,ref,alt,firth,test,nobs,orbeta,se,ci,tz,p." argument="--glm">
|
|
|
4123 <option value="no_set" selected="True">Don't set</option>
|
|
|
4124 <option value="set">Set value(s)</option>
|
|
|
4125 </param>
|
|
|
4126 <when value="no_set">
|
|
|
4127 </when>
|
|
|
4128 <when value="set">
|
|
|
4129
|
|
|
4130 <param name="glm_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
4131 <param name="glm_MOD_1_0" type="text" label="'omit-ref'" value="" optional="False" argument="'omit-ref'" help=""/>
|
|
|
4132 <conditional name="CONDITIONAL_glm_MOD_2">
|
|
|
4133 <param name="CONDITIONAL_SELECT_glm_MOD_2" type="select" label="How to set Glm">
|
|
|
4134 <option value="no_set" selected="True">Don't set</option>
|
|
|
4135 <option value="from_list">Select from list</option>
|
|
|
4136
|
|
|
4137 </param>
|
|
|
4138 <when value="no_set">
|
|
|
4139 </when>
|
|
|
4140
|
|
|
4141 <when value="from_list">
|
|
|
4142 <param name="glm_MOD_2" type="select" label="Select value">
|
|
1
|
4143 <option value="{sex"><![CDATA[{sex]]></option>
|
|
|
4144 <option value="no-x-sex}"><![CDATA[no-x-sex}]]></option>
|
|
0
|
4145 </param>
|
|
|
4146 </when>
|
|
|
4147 </conditional>
|
|
|
4148 <param name="glm_MOD_3_0" type="text" label="'log10'" value="" optional="False" argument="'log10'" help=""/>
|
|
|
4149 <param name="glm_MOD_4_0" type="text" label="'pheno-ids'" value="" optional="False" argument="'pheno-ids'" help=""/>
|
|
|
4150 </when>
|
|
|
4151 </conditional>
|
|
|
4152 <conditional name="CONDITIONAL_score">
|
|
|
4153 <param name="CONDITIONAL_SELECT_score" type="select" label="Set Score" help="Apply linear scoring system(s) to each sample. The input file should have one line per scored variant. Variant IDs are read from column #i and allele codes are read from column #j, where i defaults to 1 and j defaults to i+1. For now, only one allele per multiallelic variant may be assigned an explicit score; contact us if you need this changed. * By default, a single column of input coefficients is read from column #k, where k defaults to j+1. (--score-col-nums can be used to specify multiple columns.) * 'header-read' causes the first line of the input file to be treated as a header line containing score names. Otherwise, score(s) are assigned the names 'SCORE1', 'SCORE2', etc.; and 'header' just causes the first line to be entirely ignored. * By default, copies of unnamed alleles contribute zero to score, while missing genotypes contribute an amount proportional to the loaded (via --read-freq) or imputed allele frequency. To throw out missing observations instead (decreasing the denominator in the final average when this happens), use the 'no-mean-imputation' modifier. * You can use the 'center' modifier to shift all genotypes to mean zero, or 'variance-standardize' to linearly transform the genotypes to mean-0, variance-1. * The 'dominant' modifier causes dosages greater than 1 to be treated as 1, while 'recessive' uses max(dosage - 1, 0) on diploid chromosomes. ('dominant', 'recessive', and 'variance-standardize' cannot be used with chrX.) * The 'se' modifier causes the input coefficients to be treated as independent standard errors; in this case, standard errors for the score average/sum are reported. (Note that this will systematically underestimate standard errors when scored variants are in LD.) * By default, --score errors out if a variant ID in the input file appears multiple times in the main dataset. Use the 'ignore-dup-ids' modifier to skip them instead (a warning is still printed if such variants are present). * The 'list-variants[-zs]' modifier causes variant IDs used for scoring to be written to <output prefix>.sscore.vars[.zst]. The main report supports the following column sets: maybefid: FID, if that column was in the input. fid: Force FID column to be written even when absent in the input. (IID is always present, and positioned here.) maybesid: SID, if that column was in the input. sid: Force SID column to be written even when absent in the input. pheno1: First active phenotype. phenos: All active phenotypes, if any. nmissallele: Number of nonmissing alleles. denom: Denominator of score average (equal to nmissallele value when 'no-mean-imputation' specified). dosagesum: Sum of named allele dosages. scoreavgs: Score averages. scoresums: Score sums. The default is maybefid,maybesid,phenos,nmissallele,dosagesum,scoreavgs. For more sophisticated polygenic risk scoring, we recommend the PRSice-2 software package (https://www.prsice.info/ )." argument="--score">
|
|
|
4154 <option value="no_set" selected="True">Don't set</option>
|
|
|
4155 <option value="set">Set value(s)</option>
|
|
|
4156 </param>
|
|
|
4157 <when value="no_set">
|
|
|
4158 </when>
|
|
|
4159 <when value="set">
|
|
|
4160
|
|
|
4161 <param name="score_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
4162 <param name="score_MOD_1_0" type="text" label="i" value="" optional="False" argument="i" help=""/>
|
|
|
4163 <param name="score_MOD_2_0" type="text" label="j" value="" optional="False" argument="j" help=""/>
|
|
|
4164 <param name="score_MOD_3_0" type="text" label="k" value="" optional="False" argument="k" help=""/>
|
|
|
4165 <conditional name="CONDITIONAL_score_MOD_4">
|
|
|
4166 <param name="CONDITIONAL_SELECT_score_MOD_4" type="select" label="How to set Score">
|
|
|
4167 <option value="no_set" selected="True">Don't set</option>
|
|
|
4168 <option value="from_list">Select from list</option>
|
|
|
4169
|
|
|
4170 </param>
|
|
|
4171 <when value="no_set">
|
|
|
4172 </when>
|
|
|
4173
|
|
|
4174 <when value="from_list">
|
|
|
4175 <param name="score_MOD_4" type="select" label="Select value">
|
|
1
|
4176 <option value="{header"><![CDATA[{header]]></option>
|
|
|
4177 <option value="header-read}"><![CDATA[header-read}]]></option>
|
|
0
|
4178 </param>
|
|
|
4179 </when>
|
|
|
4180 </conditional>
|
|
|
4181 <conditional name="CONDITIONAL_score_MOD_5">
|
|
|
4182 <param name="CONDITIONAL_SELECT_score_MOD_5" type="select" label="How to set Score">
|
|
|
4183 <option value="no_set" selected="True">Don't set</option>
|
|
|
4184 <option value="from_list">Select from list</option>
|
|
|
4185
|
|
|
4186 </param>
|
|
|
4187 <when value="no_set">
|
|
|
4188 </when>
|
|
|
4189
|
|
|
4190 <when value="from_list">
|
|
|
4191 <param name="score_MOD_5" type="select" label="Select value">
|
|
1
|
4192 <option value="{center"><![CDATA[{center]]></option>
|
|
|
4193 <option value="variance-standardize"><![CDATA[variance-standardize]]></option>
|
|
|
4194 <option value="dominant"><![CDATA[dominant]]></option>
|
|
|
4195 <option value="recessive}"><![CDATA[recessive}]]></option>
|
|
0
|
4196 </param>
|
|
|
4197 </when>
|
|
|
4198 </conditional>
|
|
|
4199 <param name="score_MOD_6_0" type="text" label="'no-mean-imputation'" value="" optional="False" argument="'no-mean-imputation'" help=""/>
|
|
|
4200 <param name="score_MOD_7_0" type="text" label="'se'" value="" optional="False" argument="'se'" help=""/>
|
|
|
4201 <param name="score_MOD_8_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
4202 <param name="score_MOD_9_0" type="text" label="'ignore-dup-ids'" value="" optional="False" argument="'ignore-dup-ids'" help=""/>
|
|
|
4203 <conditional name="CONDITIONAL_score_MOD_10">
|
|
|
4204 <param name="CONDITIONAL_SELECT_score_MOD_10" type="select" label="How to set Score">
|
|
|
4205 <option value="no_set" selected="True">Don't set</option>
|
|
|
4206 <option value="from_list">Select from list</option>
|
|
|
4207
|
|
|
4208 </param>
|
|
|
4209 <when value="no_set">
|
|
|
4210 </when>
|
|
|
4211
|
|
|
4212 <when value="from_list">
|
|
|
4213 <param name="score_MOD_10" type="select" label="Select value">
|
|
1
|
4214 <option value="{list-variants"><![CDATA[{list-variants]]></option>
|
|
|
4215 <option value="list-variants-zs}"><![CDATA[list-variants-zs}]]></option>
|
|
0
|
4216 </param>
|
|
|
4217 </when>
|
|
|
4218 </conditional>
|
|
|
4219 <param name="score_MOD_11_0" type="text" label="'cols='<col set descriptor>" value="" optional="False" argument="'cols='<col set descriptor>" help=""/>
|
|
|
4220 </when>
|
|
|
4221 </conditional>
|
|
|
4222 <conditional name="CONDITIONAL_variant_score">
|
|
|
4223 <param name="CONDITIONAL_SELECT_variant_score" type="select" label="Set Variant score" help="(alias: --vscore) Apply linear scoring system(s) to each variant. Each reported variant score is the dot product of a sample-weight vector with the total-ALT-dosage vector, with MAF-based mean imputation applied to missing dosages. Input file format: one line per sample, each starting with an ID and followed by scoring weight(s); it can also have a header line with the sample ID representation and the score name(s). The usual .vscore text report supports the following column sets: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. altfreq: ALT allele frequency used for mean-imputation. nmiss: Number of missing (and thus mean-imputed) dosages. nobs: Number of (nonmissing) sample observations. (Variant scores are always present, and positioned here.) Default is chrom,pos,ref,alt. If binary output is requested instead, the main .vscore.bin matrix contains double-precision floating-point values, column (score) ID(s) are saved to a <output prefix>.vscore.cols, and variant IDs are saved to <output prefix>.vscore.vars[.zst]." argument="--variant-score">
|
|
|
4224 <option value="no_set" selected="True">Don't set</option>
|
|
|
4225 <option value="set">Set value(s)</option>
|
|
|
4226 </param>
|
|
|
4227 <when value="no_set">
|
|
|
4228 </when>
|
|
|
4229 <when value="set">
|
|
|
4230
|
|
|
4231 <param name="variant_score_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
4232 <param name="variant_score_MOD_1_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
4233 <conditional name="CONDITIONAL_variant_score_MOD_2">
|
|
|
4234 <param name="CONDITIONAL_SELECT_variant_score_MOD_2" type="select" label="How to set Variant score">
|
|
|
4235 <option value="no_set" selected="True">Don't set</option>
|
|
|
4236 <option value="from_list">Select from list</option>
|
|
|
4237
|
|
|
4238 </param>
|
|
|
4239 <when value="no_set">
|
|
|
4240 </when>
|
|
|
4241
|
|
|
4242 <when value="from_list">
|
|
|
4243 <param name="variant_score_MOD_2" type="select" label="Select value">
|
|
1
|
4244 <option value="'bin'"><![CDATA['bin']]></option>
|
|
|
4245 <option value="'cols='<col set descriptor>"><![CDATA['cols='<col set descriptor>]]></option>
|
|
0
|
4246 </param>
|
|
|
4247 </when>
|
|
|
4248 </conditional>
|
|
|
4249 </when>
|
|
|
4250 </conditional>
|
|
|
4251 <conditional name="CONDITIONAL_adjust_file">
|
|
|
4252 <param name="CONDITIONAL_SELECT_adjust_file" type="select" label="Set Adjust file" help="Given a file with unfiltered association test results, report some basic multiple-testing corrections, sorted in increasing-p-value order. * 'gc' causes genomic-controlled p-values to be used in the formulas. (This tends to be overly conservative. We note that LD Score regression usually does a better job of calibrating lambda; see Lee JJ, McGue M, Iacono WG, Chow CC (2018) The accuracy of LD Score regression as an estimator of confounding and genetic correlations in genome-wide association studies.) * 'log10' causes negative base 10 logs of p-values to be reported, instead of raw p-values. 'input-log10' specifies that the input file contains -log10(p) values. * If the input file contains multiple tests per variant which are distinguished by a 'TEST' column (true for --linear/--logistic/--glm), you must use 'test=' to select the test to process. The following column sets are supported: chrom: Chromosome ID. pos: Base-pair coordinate. (ID is always present, and positioned here.) ref: Reference allele. alt1: Alternate allele 1. alt: All alternate alleles, comma-separated. a1: Tested allele. (Omitted if missing from input file.) unadj: Unadjusted p-value. gc: Devlin & Roeder (1999) genomic control corrected p-value (additive models only). qq: P-value quantile. bonf: Bonferroni correction. holm: Holm-Bonferroni (1979) adjusted p-value. sidakss: Sidak single-step adjusted p-value. sidaksd: Sidak step-down adjusted p-value. fdrbh: Benjamini & Hochberg (1995) step-up false discovery control. fdrby: Benjamini & Yekutieli (2001) step-up false discovery control. Default set is chrom,a1,unadj,gc,bonf,holm,sidakss,sidaksd,fdrbh,fdrby." argument="--adjust-file">
|
|
|
4253 <option value="no_set" selected="True">Don't set</option>
|
|
|
4254 <option value="set">Set value(s)</option>
|
|
|
4255 </param>
|
|
|
4256 <when value="no_set">
|
|
|
4257 </when>
|
|
|
4258 <when value="set">
|
|
|
4259
|
|
|
4260 <param name="adjust_file_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
4261 <param name="adjust_file_MOD_1_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
4262 <param name="adjust_file_MOD_2_0" type="text" label="'gc'" value="" optional="False" argument="'gc'" help=""/>
|
|
|
4263 <param name="adjust_file_MOD_3_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/>
|
|
|
4264 <param name="adjust_file_MOD_4_0" type="text" label="'log10'" value="" optional="False" argument="'log10'" help=""/>
|
|
|
4265 <param name="adjust_file_MOD_5_0" type="text" label="'input-log10'" value="" optional="False" argument="'input-log10'" help=""/>
|
|
|
4266 <param name="adjust_file_MOD_6_0" type="text" label="'test='<test name, case-sensitive>" value="" optional="False" argument="'test='<test name, case-sensitive>" help=""/>
|
|
|
4267 </when>
|
|
|
4268 </conditional>
|
|
|
4269 <conditional name="CONDITIONAL_genotyping_rate">
|
|
|
4270 <param name="CONDITIONAL_SELECT_genotyping_rate" type="select" label="Set Genotyping rate" help="Report genotyping rate in log (this was automatic in PLINK 1.x)." argument="--genotyping-rate">
|
|
|
4271 <option value="no_set" selected="True">Don't set</option>
|
|
|
4272 <option value="set">Set value(s)</option>
|
|
|
4273 </param>
|
|
|
4274 <when value="no_set">
|
|
|
4275 </when>
|
|
|
4276 <when value="set">
|
|
|
4277
|
|
|
4278 <param name="genotyping_rate_MOD_0_0" type="text" label="'dosage'" value="" optional="False" argument="'dosage'" help=""/>
|
|
|
4279 </when>
|
|
|
4280 </conditional>
|
|
|
4281 <param name="pgen_info" type="boolean" label="Pgen info" truevalue="--pgen-info" falsevalue="" optional="true" argument="--pgen-info" help="Reports basic information about a .pgen file." checked="False"/>
|
|
|
4282 <param name="validate" type="boolean" label="Validate" truevalue="--validate" falsevalue="" optional="true" argument="--validate" help="Validates all variant records in a .pgen file." checked="False"/>
|
|
|
4283 <conditional name="CONDITIONAL_zst_decompress">
|
|
|
4284 <param name="CONDITIONAL_SELECT_zst_decompress" type="select" label="Set Zst decompress" help="(alias: --zd) Decompress a Zstd-compressed file. If no output filename is specified, the file is decompressed to standard output. This cannot be used with any other flags, and does not cause a log file to be generated." argument="--zst-decompress">
|
|
|
4285 <option value="no_set" selected="True">Don't set</option>
|
|
|
4286 <option value="set">Set value(s)</option>
|
|
|
4287 </param>
|
|
|
4288 <when value="no_set">
|
|
|
4289 </when>
|
|
|
4290 <when value="set">
|
|
|
4291
|
|
|
4292 <param name="zst_decompress_MOD_0_0" type="text" label=".zst file" value="" optional="True" argument=".zst file" help=""/>
|
|
|
4293 <param name="zst_decompress_MOD_1_0" type="text" label="output filename" value="" optional="False" argument="output filename" help=""/>
|
|
|
4294 </when>
|
|
|
4295 </conditional>
|
|
|
4296 <conditional name="CONDITIONAL_silent">
|
|
|
4297 <param name="CONDITIONAL_SELECT_silent" type="select" label="Set Silent" help="Suppress regular output to console. (Error-output is not suppressed.) " argument="--silent">
|
|
|
4298 <option value="no_set" selected="True">Don't set</option>
|
|
|
4299 <option value="set">Set value(s)</option>
|
|
|
4300 </param>
|
|
|
4301 <when value="no_set">
|
|
|
4302 </when>
|
|
|
4303 <when value="set">
|
|
|
4304
|
|
|
4305 </when>
|
|
|
4306 </conditional>
|
|
|
4307 <conditional name="CONDITIONAL_double_id">
|
|
|
4308 <param name="CONDITIONAL_SELECT_double_id" type="select" label="Set Double id" help="Set both FIDs and IIDs to the VCF/.bgen sample ID. " argument="--double-id">
|
|
|
4309 <option value="no_set" selected="True">Don't set</option>
|
|
|
4310 <option value="set">Set value(s)</option>
|
|
|
4311 </param>
|
|
|
4312 <when value="no_set">
|
|
|
4313 </when>
|
|
|
4314 <when value="set">
|
|
|
4315
|
|
|
4316 </when>
|
|
|
4317 </conditional>
|
|
|
4318 <conditional name="CONDITIONAL_const_fid">
|
|
|
4319 <param name="CONDITIONAL_SELECT_const_fid" type="select" label="Set Const fid" help="Set all FIDs to the given constant. If '0' (the default), no FID column is created. " argument="--const-fid">
|
|
|
4320 <option value="no_set" selected="True">Don't set</option>
|
|
|
4321 <option value="set">Set value(s)</option>
|
|
|
4322 </param>
|
|
|
4323 <when value="no_set">
|
|
|
4324 </when>
|
|
|
4325 <when value="set">
|
|
|
4326
|
|
|
4327 <param name="const_fid_MOD_0_0" type="text" label="ID" value="" optional="False" argument="ID" help=""/>
|
|
|
4328 </when>
|
|
|
4329 </conditional>
|
|
|
4330 <conditional name="CONDITIONAL_id_delim">
|
|
|
4331 <param name="CONDITIONAL_SELECT_id_delim" type="select" label="Set Id delim" help="Normally parses single-delimiter sample IDs as <FID><d><IID>, and double-delimiter IDs as <FID><d><IID><d><SID>; default delimiter is '_'. --id-delim can no longer be used with --double-id/--const-fid; it will error out if any ID lacks the delimiter. " argument="--id-delim">
|
|
|
4332 <option value="no_set" selected="True">Don't set</option>
|
|
|
4333 <option value="set">Set value(s)</option>
|
|
|
4334 </param>
|
|
|
4335 <when value="no_set">
|
|
|
4336 </when>
|
|
|
4337 <when value="set">
|
|
|
4338
|
|
|
4339 <param name="id_delim_MOD_0_0" type="text" label="d" value="" optional="False" argument="d" help=""/>
|
|
|
4340 </when>
|
|
|
4341 </conditional>
|
|
|
4342 <conditional name="CONDITIONAL_idspace_to">
|
|
|
4343 <param name="CONDITIONAL_SELECT_idspace_to" type="select" label="Set Idspace to" help="Convert spaces in VCF/.bgen sample IDs to the given character. " argument="--idspace-to">
|
|
|
4344 <option value="no_set" selected="True">Don't set</option>
|
|
|
4345 <option value="set">Set value(s)</option>
|
|
|
4346 </param>
|
|
|
4347 <when value="no_set">
|
|
|
4348 </when>
|
|
|
4349 <when value="set">
|
|
|
4350
|
|
|
4351 <param name="idspace_to_MOD_0_0" type="text" label="c" value="" optional="True" argument="c" help=""/>
|
|
|
4352 </when>
|
|
|
4353 </conditional>
|
|
|
4354 <conditional name="CONDITIONAL_iid_sid">
|
|
|
4355 <param name="CONDITIONAL_SELECT_iid_sid" type="select" label="Set Iid sid" help="Make --id-delim and --sample-diff interpret two-token sample IDs as IID-SID instead of FID-IID. " argument="--iid-sid">
|
|
|
4356 <option value="no_set" selected="True">Don't set</option>
|
|
|
4357 <option value="set">Set value(s)</option>
|
|
|
4358 </param>
|
|
|
4359 <when value="no_set">
|
|
|
4360 </when>
|
|
|
4361 <when value="set">
|
|
|
4362
|
|
|
4363 </when>
|
|
|
4364 </conditional>
|
|
|
4365 <conditional name="CONDITIONAL_vcf_require_gt">
|
|
|
4366 <param name="CONDITIONAL_SELECT_vcf_require_gt" type="select" label="Set Vcf require gt" help="Skip variants with no GT field. " argument="--vcf-require-gt">
|
|
|
4367 <option value="no_set" selected="True">Don't set</option>
|
|
|
4368 <option value="set">Set value(s)</option>
|
|
|
4369 </param>
|
|
|
4370 <when value="no_set">
|
|
|
4371 </when>
|
|
|
4372 <when value="set">
|
|
|
4373
|
|
|
4374 </when>
|
|
|
4375 </conditional>
|
|
|
4376 <conditional name="CONDITIONAL_vcf_min_gq">
|
|
|
4377 <param name="CONDITIONAL_SELECT_vcf_min_gq" type="select" label="Set Vcf min gq" help="No-call genotypes when GQ is present and below the threshold. " argument="--vcf-min-gq">
|
|
|
4378 <option value="no_set" selected="True">Don't set</option>
|
|
|
4379 <option value="set">Set value(s)</option>
|
|
|
4380 </param>
|
|
|
4381 <when value="no_set">
|
|
|
4382 </when>
|
|
|
4383 <when value="set">
|
|
|
4384
|
|
|
4385 <param name="vcf_min_gq_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
4386 </when>
|
|
|
4387 </conditional>
|
|
|
4388 <conditional name="CONDITIONAL_vcf_max_dp">
|
|
|
4389 <param name="CONDITIONAL_SELECT_vcf_max_dp" type="select" label="Set Vcf max dp" help="No-call genotypes when DP is present and above/below " argument="--vcf-max-dp">
|
|
|
4390 <option value="no_set" selected="True">Don't set</option>
|
|
|
4391 <option value="set">Set value(s)</option>
|
|
|
4392 </param>
|
|
|
4393 <when value="no_set">
|
|
|
4394 </when>
|
|
|
4395 <when value="set">
|
|
|
4396
|
|
|
4397 <param name="vcf_max_dp_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
4398 </when>
|
|
|
4399 </conditional>
|
|
|
4400 <conditional name="CONDITIONAL_vcf_min_dp">
|
|
|
4401 <param name="CONDITIONAL_SELECT_vcf_min_dp" type="select" label="Set Vcf min dp" help="" argument="--vcf-min-dp">
|
|
|
4402 <option value="no_set" selected="True">Don't set</option>
|
|
|
4403 <option value="set">Set value(s)</option>
|
|
|
4404 </param>
|
|
|
4405 <when value="no_set">
|
|
|
4406 </when>
|
|
|
4407 <when value="set">
|
|
|
4408
|
|
|
4409 <param name="vcf_min_dp_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
4410 </when>
|
|
|
4411 </conditional>
|
|
|
4412 <conditional name="CONDITIONAL_vcf_half_call">
|
|
|
4413 <param name="CONDITIONAL_SELECT_vcf_half_call" type="select" label="Set Vcf half call" help="Specify how '0/.' and similar VCF GT values should be handled. The following four modes are supported: * 'error'/'e' (default) errors out and reports line #. * 'haploid'/'h' treats them as haploid calls. * 'missing'/'m' treats them as missing. * 'reference'/'r' treats the missing value as 0. " argument="--vcf-half-call">
|
|
|
4414 <option value="no_set" selected="True">Don't set</option>
|
|
|
4415 <option value="set">Set value(s)</option>
|
|
|
4416 </param>
|
|
|
4417 <when value="no_set">
|
|
|
4418 </when>
|
|
|
4419 <when value="set">
|
|
|
4420
|
|
|
4421 <param name="vcf_half_call_MOD_0_0" type="text" label="m" value="" optional="True" argument="m" help=""/>
|
|
|
4422 </when>
|
|
|
4423 </conditional>
|
|
|
4424 <conditional name="CONDITIONAL_oxford_single_chr">
|
|
|
4425 <param name="CONDITIONAL_SELECT_oxford_single_chr" type="select" label="Set Oxford single chr" help="Specify single-chromosome .gen/.bgen file with no useful chromosome info inside. " argument="--oxford-single-chr">
|
|
|
4426 <option value="no_set" selected="True">Don't set</option>
|
|
|
4427 <option value="set">Set value(s)</option>
|
|
|
4428 </param>
|
|
|
4429 <when value="no_set">
|
|
|
4430 </when>
|
|
|
4431 <when value="set">
|
|
|
4432
|
|
|
4433 <param name="oxford_single_chr_MOD_0_0" type="text" label="chr name" value="" optional="True" argument="chr name" help=""/>
|
|
|
4434 </when>
|
|
|
4435 </conditional>
|
|
|
4436 <conditional name="CONDITIONAL_missing_code">
|
|
|
4437 <param name="CONDITIONAL_SELECT_missing_code" type="select" label="Set Missing code" help="Comma-delimited list of missing phenotype (alias: --missing_code) values for Oxford-format import (default 'NA')." argument="--missing-code">
|
|
|
4438 <option value="no_set" selected="True">Don't set</option>
|
|
|
4439 <option value="set">Set value(s)</option>
|
|
|
4440 </param>
|
|
|
4441 <when value="no_set">
|
|
|
4442 </when>
|
|
|
4443 <when value="set">
|
|
|
4444
|
|
|
4445 <param name="missing_code_MOD_0_0" type="text" label="string list" value="" optional="False" argument="string list" help=""/>
|
|
|
4446 </when>
|
|
|
4447 </conditional>
|
|
|
4448 <conditional name="CONDITIONAL_hard_call_threshold">
|
|
|
4449 <param name="CONDITIONAL_SELECT_hard_call_threshold" type="select" label="Set Hard call threshold" help="When importing dosage data, a hardcall is normally saved when the distance from the nearest hardcall, defined as 0.5 * sum_i |x_i - round(x_i)| (where the x_i's are 0..2 allele dosages), is not greater than 0.1. You can adjust this threshold by providing a numeric parameter to --hard-call-threshold. You can also use this with --make-[b]pgen to alter the saved hardcalls while leaving the dosages untouched, or --make-bed to tweak hardcall export. " argument="--hard-call-threshold">
|
|
|
4450 <option value="no_set" selected="True">Don't set</option>
|
|
|
4451 <option value="set">Set value(s)</option>
|
|
|
4452 </param>
|
|
|
4453 <when value="no_set">
|
|
|
4454 </when>
|
|
|
4455 <when value="set">
|
|
|
4456
|
|
|
4457 <param name="hard_call_threshold_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
4458 </when>
|
|
|
4459 </conditional>
|
|
|
4460 <conditional name="CONDITIONAL_dosage_erase_threshold">
|
|
|
4461 <param name="CONDITIONAL_SELECT_dosage_erase_threshold" type="select" label="Set Dosage erase threshold" help="--hard-call-threshold normally preserves the original dosages, and several PLINK 2 commands use them when they're available. Use --dosage-erase-threshold to make PLINK 2 erase dosages and keep only hardcalls when distance-from-hardcall <= the given level. " argument="--dosage-erase-threshold">
|
|
|
4462 <option value="no_set" selected="True">Don't set</option>
|
|
|
4463 <option value="set">Set value(s)</option>
|
|
|
4464 </param>
|
|
|
4465 <when value="no_set">
|
|
|
4466 </when>
|
|
|
4467 <when value="set">
|
|
|
4468
|
|
|
4469 <param name="dosage_erase_threshold_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
4470 </when>
|
|
|
4471 </conditional>
|
|
|
4472 <conditional name="CONDITIONAL_import_dosage_certainty">
|
|
|
4473 <param name="CONDITIONAL_SELECT_import_dosage_certainty" type="select" label="Set Import dosage certainty" help="The PLINK 2 file format currently supports a single dosage for each allele. Some other dosage file formats include a separate probability for every possible genotype, e.g. {P(0/0)=0.2, P(0/1)=0.52, P(1/1)=0.28}, a highly uncertain call that is nevertheless treated as a hardcall under '--hard-call-threshold 0.1'. To make PLINK 2 treat a dosage as missing whenever the largest probability is less than a threshold, use --import-dosage-certainty. " argument="--import-dosage-certainty">
|
|
|
4474 <option value="no_set" selected="True">Don't set</option>
|
|
|
4475 <option value="set">Set value(s)</option>
|
|
|
4476 </param>
|
|
|
4477 <when value="no_set">
|
|
|
4478 </when>
|
|
|
4479 <when value="set">
|
|
|
4480
|
|
|
4481 <param name="import_dosage_certainty_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
4482 </when>
|
|
|
4483 </conditional>
|
|
|
4484 <conditional name="CONDITIONAL_input_missing_genotype">
|
|
|
4485 <param name="CONDITIONAL_SELECT_input_missing_genotype" type="select" label="Set Input missing genotype" help="'.' is always interpreted as a missing genotype code in input files. By default, '0' also is; you can change this second missing code with --input-missing-genotype. " argument="--input-missing-genotype">
|
|
|
4486 <option value="no_set" selected="True">Don't set</option>
|
|
|
4487 <option value="set">Set value(s)</option>
|
|
|
4488 </param>
|
|
|
4489 <when value="no_set">
|
|
|
4490 </when>
|
|
|
4491 <when value="set">
|
|
|
4492
|
|
|
4493 <param name="input_missing_genotype_MOD_0_0" type="text" label="c" value="" optional="True" argument="c" help=""/>
|
|
|
4494 </when>
|
|
|
4495 </conditional>
|
|
|
4496 <conditional name="CONDITIONAL_allow_extra_chr">
|
|
|
4497 <param name="CONDITIONAL_SELECT_allow_extra_chr" type="select" label="Set Allow extra chr" help="Permit unrecognized chromosome codes (alias --aec). " argument="--allow-extra-chr">
|
|
|
4498 <option value="no_set" selected="True">Don't set</option>
|
|
|
4499 <option value="set">Set value(s)</option>
|
|
|
4500 </param>
|
|
|
4501 <when value="no_set">
|
|
|
4502 </when>
|
|
|
4503 <when value="set">
|
|
|
4504
|
|
|
4505 </when>
|
|
|
4506 </conditional>
|
|
|
4507 <conditional name="CONDITIONAL_chr_set">
|
|
|
4508 <param name="CONDITIONAL_SELECT_chr_set" type="select" label="Set Chr set" help="Specify a nonhuman chromosome set. The first parameter sets the number of diploid autosome pairs if positive, or haploid chromosomes if negative. Given diploid autosomes, the remaining modifiers indicate the absence of the named non-autosomal chromosomes." argument="--chr-set">
|
|
|
4509 <option value="no_set" selected="True">Don't set</option>
|
|
|
4510 <option value="set">Set value(s)</option>
|
|
|
4511 </param>
|
|
|
4512 <when value="no_set">
|
|
|
4513 </when>
|
|
|
4514 <when value="set">
|
|
|
4515
|
|
|
4516 <param name="chr_set_MOD_0_0" type="text" label="autosome ct" value="" optional="True" argument="autosome ct" help=""/>
|
|
|
4517 <param name="chr_set_MOD_1_0" type="text" label="'no-x'" value="" optional="False" argument="'no-x'" help=""/>
|
|
|
4518 <param name="chr_set_MOD_2_0" type="text" label="'no-y'" value="" optional="False" argument="'no-y'" help=""/>
|
|
|
4519 <param name="chr_set_MOD_3_0" type="text" label="'no-xy'" value="" optional="False" argument="'no-xy'" help=""/>
|
|
|
4520 <param name="chr_set_MOD_4_0" type="text" label="'no-mt'" value="" optional="False" argument="'no-mt'" help=""/>
|
|
|
4521 </when>
|
|
|
4522 </conditional>
|
|
|
4523 <conditional name="CONDITIONAL_cow">
|
|
|
4524 <param name="CONDITIONAL_SELECT_cow" type="select" label="Set Cow" help="Shortcuts for those species. " argument="--cow">
|
|
|
4525 <option value="no_set" selected="True">Don't set</option>
|
|
|
4526 <option value="set">Set value(s)</option>
|
|
|
4527 </param>
|
|
|
4528 <when value="no_set">
|
|
|
4529 </when>
|
|
|
4530 <when value="set">
|
|
|
4531
|
|
|
4532 </when>
|
|
|
4533 </conditional>
|
|
|
4534 <conditional name="CONDITIONAL_dog">
|
|
|
4535 <param name="CONDITIONAL_SELECT_dog" type="select" label="Set Dog" help="Shortcuts for those species. " argument="--dog">
|
|
|
4536 <option value="no_set" selected="True">Don't set</option>
|
|
|
4537 <option value="set">Set value(s)</option>
|
|
|
4538 </param>
|
|
|
4539 <when value="no_set">
|
|
|
4540 </when>
|
|
|
4541 <when value="set">
|
|
|
4542
|
|
|
4543 </when>
|
|
|
4544 </conditional>
|
|
|
4545 <conditional name="CONDITIONAL_horse">
|
|
|
4546 <param name="CONDITIONAL_SELECT_horse" type="select" label="Set Horse" help="Shortcuts for those species. " argument="--horse">
|
|
|
4547 <option value="no_set" selected="True">Don't set</option>
|
|
|
4548 <option value="set">Set value(s)</option>
|
|
|
4549 </param>
|
|
|
4550 <when value="no_set">
|
|
|
4551 </when>
|
|
|
4552 <when value="set">
|
|
|
4553
|
|
|
4554 </when>
|
|
|
4555 </conditional>
|
|
|
4556 <conditional name="CONDITIONAL_mouse">
|
|
|
4557 <param name="CONDITIONAL_SELECT_mouse" type="select" label="Set Mouse" help="Shortcuts for those species. " argument="--mouse">
|
|
|
4558 <option value="no_set" selected="True">Don't set</option>
|
|
|
4559 <option value="set">Set value(s)</option>
|
|
|
4560 </param>
|
|
|
4561 <when value="no_set">
|
|
|
4562 </when>
|
|
|
4563 <when value="set">
|
|
|
4564
|
|
|
4565 </when>
|
|
|
4566 </conditional>
|
|
|
4567 <conditional name="CONDITIONAL_rice">
|
|
|
4568 <param name="CONDITIONAL_SELECT_rice" type="select" label="Set Rice" help="Shortcuts for those species. " argument="--rice">
|
|
|
4569 <option value="no_set" selected="True">Don't set</option>
|
|
|
4570 <option value="set">Set value(s)</option>
|
|
|
4571 </param>
|
|
|
4572 <when value="no_set">
|
|
|
4573 </when>
|
|
|
4574 <when value="set">
|
|
|
4575
|
|
|
4576 </when>
|
|
|
4577 </conditional>
|
|
|
4578 <conditional name="CONDITIONAL_sheep">
|
|
|
4579 <param name="CONDITIONAL_SELECT_sheep" type="select" label="Set Sheep" help="Shortcuts for those species. " argument="--sheep">
|
|
|
4580 <option value="no_set" selected="True">Don't set</option>
|
|
|
4581 <option value="set">Set value(s)</option>
|
|
|
4582 </param>
|
|
|
4583 <when value="no_set">
|
|
|
4584 </when>
|
|
|
4585 <when value="set">
|
|
|
4586
|
|
|
4587 </when>
|
|
|
4588 </conditional>
|
|
|
4589 <conditional name="CONDITIONAL_autosome_num">
|
|
|
4590 <param name="CONDITIONAL_SELECT_autosome_num" type="select" label="Set Autosome num" help="Alias for '--chr-set <value> no-y no-xy no-mt'. " argument="--autosome-num">
|
|
|
4591 <option value="no_set" selected="True">Don't set</option>
|
|
|
4592 <option value="set">Set value(s)</option>
|
|
|
4593 </param>
|
|
|
4594 <when value="no_set">
|
|
|
4595 </when>
|
|
|
4596 <when value="set">
|
|
|
4597
|
|
|
4598 <param name="autosome_num_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
4599 </when>
|
|
|
4600 </conditional>
|
|
|
4601 <conditional name="CONDITIONAL_human">
|
|
|
4602 <param name="CONDITIONAL_SELECT_human" type="select" label="Set Human" help="Explicitly specify human chromosome set, and make output .pvar/VCF files include a ##chrSet header line. (.pvar/VCF output files automatically include ##chrSet when a nonhuman set is specified.) " argument="--human">
|
|
|
4603 <option value="no_set" selected="True">Don't set</option>
|
|
|
4604 <option value="set">Set value(s)</option>
|
|
|
4605 </param>
|
|
|
4606 <when value="no_set">
|
|
|
4607 </when>
|
|
|
4608 <when value="set">
|
|
|
4609
|
|
|
4610 </when>
|
|
|
4611 </conditional>
|
|
|
4612 <conditional name="CONDITIONAL_chr_override">
|
|
|
4613 <param name="CONDITIONAL_SELECT_chr_override" type="select" label="Set Chr override" help="By default, if --chr-set/--autosome-num/--cow/etc. conflicts with an input file ##chrSet header line, PLINK 2 will error out. --chr-override with no parameter causes the command line to take precedence; '--chr-override file' defers to the file. " argument="--chr-override">
|
|
|
4614 <option value="no_set" selected="True">Don't set</option>
|
|
|
4615 <option value="set">Set value(s)</option>
|
|
|
4616 </param>
|
|
|
4617 <when value="no_set">
|
|
|
4618 </when>
|
|
|
4619 <when value="set">
|
|
|
4620
|
|
|
4621 <param name="chr_override_MOD_0_0" type="text" label="'file'" value="" optional="False" argument="'file'" help=""/>
|
|
|
4622 </when>
|
|
|
4623 </conditional>
|
|
|
4624 <conditional name="CONDITIONAL_var_min_qual">
|
|
|
4625 <param name="CONDITIONAL_SELECT_var_min_qual" type="select" label="Set Var min qual" help="Skip variants with low/missing QUAL. " argument="--var-min-qual">
|
|
|
4626 <option value="no_set" selected="True">Don't set</option>
|
|
|
4627 <option value="set">Set value(s)</option>
|
|
|
4628 </param>
|
|
|
4629 <when value="no_set">
|
|
|
4630 </when>
|
|
|
4631 <when value="set">
|
|
|
4632
|
|
|
4633 <param name="var_min_qual_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
4634 </when>
|
|
|
4635 </conditional>
|
|
|
4636 <conditional name="CONDITIONAL_var_filter">
|
|
|
4637 <param name="CONDITIONAL_SELECT_var_filter" type="select" label="Set Var filter" help="Skip variants which have FILTER failures. " argument="--var-filter">
|
|
|
4638 <option value="no_set" selected="True">Don't set</option>
|
|
|
4639 <option value="set">Set value(s)</option>
|
|
|
4640 </param>
|
|
|
4641 <when value="no_set">
|
|
|
4642 </when>
|
|
|
4643 <when value="set">
|
|
|
4644
|
|
|
4645 <param name="var_filter_MOD_0_0" type="text" label="exception(s)..." value="" optional="False" argument="exception(s)..." help="Multiple values are allowed"/>
|
|
|
4646 </when>
|
|
|
4647 </conditional>
|
|
|
4648 <conditional name="CONDITIONAL_extract_if_info">
|
|
|
4649 <param name="CONDITIONAL_SELECT_extract_if_info" type="select" label="Set Extract if info" help="Exclude variants which don't/do satisfy " argument="--extract-if-info">
|
|
|
4650 <option value="no_set" selected="True">Don't set</option>
|
|
|
4651 <option value="set">Set value(s)</option>
|
|
|
4652 </param>
|
|
|
4653 <when value="no_set">
|
|
|
4654 </when>
|
|
|
4655 <when value="set">
|
|
|
4656
|
|
|
4657 <param name="extract_if_info_MOD_0_0" type="text" label="key" value="" optional="True" argument="key" help=""/>
|
|
|
4658 <param name="extract_if_info_MOD_1_0" type="text" label="op" value="" optional="True" argument="op" help=""/>
|
|
|
4659 <param name="extract_if_info_MOD_2_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
4660 </when>
|
|
|
4661 </conditional>
|
|
|
4662 <conditional name="CONDITIONAL_exclude_if_info">
|
|
|
4663 <param name="CONDITIONAL_SELECT_exclude_if_info" type="select" label="Set Exclude if info" help='(aliases: --extract-if, e.g. --exclude-if) --extract-if-info "VT == SNP" Unless the operator is !=, the predicate always evaluates to false when the key is missing.' argument="--exclude-if-info">
|
|
|
4664 <option value="no_set" selected="True">Don't set</option>
|
|
|
4665 <option value="set">Set value(s)</option>
|
|
|
4666 </param>
|
|
|
4667 <when value="no_set">
|
|
|
4668 </when>
|
|
|
4669 <when value="set">
|
|
|
4670
|
|
|
4671 <param name="exclude_if_info_MOD_0_0" type="text" label="key" value="" optional="True" argument="key" help=""/>
|
|
|
4672 <param name="exclude_if_info_MOD_1_0" type="text" label="op" value="" optional="True" argument="op" help=""/>
|
|
|
4673 <param name="exclude_if_info_MOD_2_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
4674 </when>
|
|
|
4675 </conditional>
|
|
|
4676 <conditional name="CONDITIONAL_require_info">
|
|
|
4677 <param name="CONDITIONAL_SELECT_require_info" type="select" label="Set Require info" help="Exclude variants based on nonexistence " argument="--require-info">
|
|
|
4678 <option value="no_set" selected="True">Don't set</option>
|
|
|
4679 <option value="set">Set value(s)</option>
|
|
|
4680 </param>
|
|
|
4681 <when value="no_set">
|
|
|
4682 </when>
|
|
|
4683 <when value="set">
|
|
|
4684
|
|
|
4685 <param name="require_info_MOD_0_0" type="text" label="key(s)..." value="" optional="True" argument="key(s)..." help="Multiple values are allowed"/>
|
|
|
4686 </when>
|
|
|
4687 </conditional>
|
|
|
4688 <conditional name="CONDITIONAL_require_no_info">
|
|
|
4689 <param name="CONDITIONAL_SELECT_require_no_info" type="select" label="Set Require no info" help="" argument="--require-no-info">
|
|
|
4690 <option value="no_set" selected="True">Don't set</option>
|
|
|
4691 <option value="set">Set value(s)</option>
|
|
|
4692 </param>
|
|
|
4693 <when value="no_set">
|
|
|
4694 </when>
|
|
|
4695 <when value="set">
|
|
|
4696
|
|
|
4697 <param name="require_no_info_MOD_0_0" type="text" label="key(s)..." value="" optional="True" argument="key(s)..." help="Multiple values are allowed"/>
|
|
|
4698 <param name="require_no_info_MOD_1_0" type="text" label="key" value="" optional="True" argument="key" help=""/>
|
|
|
4699 </when>
|
|
|
4700 </conditional>
|
|
|
4701 <conditional name="CONDITIONAL_extract_col_cond">
|
|
|
4702 <param name="CONDITIONAL_SELECT_extract_col_cond" type="select" label="Set Extract col cond" help="" argument="--extract-col-cond">
|
|
|
4703 <option value="no_set" selected="True">Don't set</option>
|
|
|
4704 <option value="set">Set value(s)</option>
|
|
|
4705 </param>
|
|
|
4706 <when value="no_set">
|
|
|
4707 </when>
|
|
|
4708 <when value="set">
|
|
|
4709
|
|
|
4710 <param name="extract_col_cond_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/>
|
|
|
4711 <param name="extract_col_cond_MOD_1_0" type="text" label="valcol" value="" optional="False" argument="valcol" help=""/>
|
|
|
4712 <param name="extract_col_cond_MOD_2_0" type="text" label="IDcol" value="" optional="False" argument="IDcol" help=""/>
|
|
|
4713 <param name="extract_col_cond_MOD_3_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/>
|
|
|
4714 </when>
|
|
|
4715 </conditional>
|
|
|
4716 <conditional name="CONDITIONAL_extract_col_cond_match">
|
|
|
4717 <param name="CONDITIONAL_SELECT_extract_col_cond_match" type="select" label="Set Extract col cond match" help="" argument="--extract-col-cond-match">
|
|
|
4718 <option value="no_set" selected="True">Don't set</option>
|
|
|
4719 <option value="set">Set value(s)</option>
|
|
|
4720 </param>
|
|
|
4721 <when value="no_set">
|
|
|
4722 </when>
|
|
|
4723 <when value="set">
|
|
|
4724
|
|
|
4725 <param name="extract_col_cond_match_MOD_0_0" type="text" label="(sub)string(s)..." value="" optional="True" argument="(sub)string(s)..." help="Multiple values are allowed"/>
|
|
|
4726 </when>
|
|
|
4727 </conditional>
|
|
|
4728 <conditional name="CONDITIONAL_extract_col_cond_mismatch">
|
|
|
4729 <param name="CONDITIONAL_SELECT_extract_col_cond_mismatch" type="select" label="Set Extract col cond mismatch" help="" argument="--extract-col-cond-mismatch">
|
|
|
4730 <option value="no_set" selected="True">Don't set</option>
|
|
|
4731 <option value="set">Set value(s)</option>
|
|
|
4732 </param>
|
|
|
4733 <when value="no_set">
|
|
|
4734 </when>
|
|
|
4735 <when value="set">
|
|
|
4736
|
|
|
4737 <param name="extract_col_cond_mismatch_MOD_0_0" type="text" label="(sub)string(s)..." value="" optional="True" argument="(sub)string(s)..." help="Multiple values are allowed"/>
|
|
|
4738 </when>
|
|
|
4739 </conditional>
|
|
|
4740 <param name="extract_col_cond_substr" type="boolean" label="Extract col cond substr" truevalue="--extract-col-cond-substr" falsevalue="" optional="true" argument="--extract-col-cond-substr" help="" checked="False"/>
|
|
|
4741 <conditional name="CONDITIONAL_extract_col_cond_min">
|
|
|
4742 <param name="CONDITIONAL_SELECT_extract_col_cond_min" type="select" label="Set Extract col cond min" help="" argument="--extract-col-cond-min">
|
|
|
4743 <option value="no_set" selected="True">Don't set</option>
|
|
|
4744 <option value="set">Set value(s)</option>
|
|
|
4745 </param>
|
|
|
4746 <when value="no_set">
|
|
|
4747 </when>
|
|
|
4748 <when value="set">
|
|
|
4749
|
|
|
4750 <param name="extract_col_cond_min_MOD_0_0" type="text" label="min" value="" optional="True" argument="min" help=""/>
|
|
|
4751 </when>
|
|
|
4752 </conditional>
|
|
|
4753 <conditional name="CONDITIONAL_extract_col_cond_max">
|
|
|
4754 <param name="CONDITIONAL_SELECT_extract_col_cond_max" type="select" label="Set Extract col cond max" help="Exclude all variants without a value-column entry satisfying a condition. * By default, values are read from column 2 of the file, and variant IDs are read from column 1. * Three types of conditions are supported: * When --extract-col-cond-match is specified without --extract-col-cond-substr, the value is checked for equality with the given strings, and kept iff one of them matches. Similarly, --extract-col-cond-mismatch without --extract-col-cond-substr causes the variant to be kept iff the value matches none of the given strings. * When --extract-col-cond-match and/or -mismatch are specified with --extract-col-cond-substr, the variant is kept iff none of the --extract-col-cond-mismatch substrings are contained in the value, and either --extract-col-cond-match was unspecified or at least one of its substrings is contained. * Otherwise, the value is interpreted as a number, and the variant is kept if the number is in [<min>, <max>] (default min=0, max=DBL_MAX)." argument="--extract-col-cond-max">
|
|
|
4755 <option value="no_set" selected="True">Don't set</option>
|
|
|
4756 <option value="set">Set value(s)</option>
|
|
|
4757 </param>
|
|
|
4758 <when value="no_set">
|
|
|
4759 </when>
|
|
|
4760 <when value="set">
|
|
|
4761
|
|
|
4762 <param name="extract_col_cond_max_MOD_0_0" type="text" label="max" value="" optional="True" argument="max" help=""/>
|
|
|
4763 </when>
|
|
|
4764 </conditional>
|
|
|
4765 <conditional name="CONDITIONAL_pheno">
|
|
|
4766 <param name="CONDITIONAL_SELECT_pheno" type="select" label="Set Pheno" help="Specify additional phenotype/covariate file. Comma-delimited files with a header line are now permitted. " argument="--pheno">
|
|
|
4767 <option value="no_set" selected="True">Don't set</option>
|
|
|
4768 <option value="set">Set value(s)</option>
|
|
|
4769 </param>
|
|
|
4770 <when value="no_set">
|
|
|
4771 </when>
|
|
|
4772 <when value="set">
|
|
|
4773
|
|
|
4774 <param name="pheno_MOD_0_0" type="text" label="'iid-only'" value="" optional="False" argument="'iid-only'" help=""/>
|
|
|
4775 <param name="pheno_MOD_1_0" type="data" format="plink.pheno" label="f" multiple="False" optional="True" argument="f"/>
|
|
|
4776 </when>
|
|
|
4777 </conditional>
|
|
|
4778 <conditional name="CONDITIONAL_pheno_name">
|
|
|
4779 <param name="CONDITIONAL_SELECT_pheno_name" type="select" label="Set Pheno name" help="Only load the designated phenotype(s) from the --pheno (if one was specified) or .psam (if no --pheno) file. Separate multiple names with spaces or commas, and use dashes to designate ranges. " argument="--pheno-name">
|
|
|
4780 <option value="no_set" selected="True">Don't set</option>
|
|
|
4781 <option value="set">Set value(s)</option>
|
|
|
4782 </param>
|
|
|
4783 <when value="no_set">
|
|
|
4784 </when>
|
|
|
4785 <when value="set">
|
|
|
4786
|
|
|
4787 <param name="pheno_name_MOD_0_0" type="text" label="name..." value="" optional="True" argument="name..." help="Multiple values are allowed"/>
|
|
|
4788 </when>
|
|
|
4789 </conditional>
|
|
|
4790 <conditional name="CONDITIONAL_pheno_col_nums">
|
|
|
4791 <param name="CONDITIONAL_SELECT_pheno_col_nums" type="select" label="Set Pheno col nums" help="Only load the phenotype(s) in the designated column number(s) from the --pheno file. " argument="--pheno-col-nums">
|
|
|
4792 <option value="no_set" selected="True">Don't set</option>
|
|
|
4793 <option value="set">Set value(s)</option>
|
|
|
4794 </param>
|
|
|
4795 <when value="no_set">
|
|
|
4796 </when>
|
|
|
4797 <when value="set">
|
|
|
4798
|
|
|
4799 <param name="pheno_col_nums_MOD_0_0" type="text" label="#..." value="" optional="True" argument="#..." help="Multiple values are allowed"/>
|
|
|
4800 </when>
|
|
|
4801 </conditional>
|
|
|
4802 <conditional name="CONDITIONAL_no_psam_pheno">
|
|
|
4803 <param name="CONDITIONAL_SELECT_no_psam_pheno" type="select" label="Set No psam pheno" help="Ignore phenotype(s) in .psam/.fam file. " argument="--no-psam-pheno">
|
|
|
4804 <option value="no_set" selected="True">Don't set</option>
|
|
|
4805 <option value="set">Set value(s)</option>
|
|
|
4806 </param>
|
|
|
4807 <when value="no_set">
|
|
|
4808 </when>
|
|
|
4809 <when value="set">
|
|
|
4810
|
|
|
4811 </when>
|
|
|
4812 </conditional>
|
|
|
4813 <conditional name="CONDITIONAL_strict_sid0">
|
|
|
4814 <param name="CONDITIONAL_SELECT_strict_sid0" type="select" label="Set Strict sid0" help="By default, if there is no SID column in the .psam/.fam (or --update-ids) file, but there is one in another input file (for e.g. --keep/--remove), the latter SID column is ignored; sample IDs are considered matching as long as FID and IID are equal (with missing FID treated as '0'). If you also want to require SID = '0' for a sample ID match in this situation, add --strict-sid0. " argument="--strict-sid0">
|
|
|
4815 <option value="no_set" selected="True">Don't set</option>
|
|
|
4816 <option value="set">Set value(s)</option>
|
|
|
4817 </param>
|
|
|
4818 <when value="no_set">
|
|
|
4819 </when>
|
|
|
4820 <when value="set">
|
|
|
4821
|
|
|
4822 </when>
|
|
|
4823 </conditional>
|
|
|
4824 <conditional name="CONDITIONAL_input_missing_phenotype">
|
|
|
4825 <param name="CONDITIONAL_SELECT_input_missing_phenotype" type="select" label="Set Input missing phenotype" help="Set nonzero number to treat as a missing pheno/covar in input files (default -9). " argument="--input-missing-phenotype">
|
|
|
4826 <option value="no_set" selected="True">Don't set</option>
|
|
|
4827 <option value="set">Set value(s)</option>
|
|
|
4828 </param>
|
|
|
4829 <when value="no_set">
|
|
|
4830 </when>
|
|
|
4831 <when value="set">
|
|
|
4832
|
|
|
4833 <param name="input_missing_phenotype_MOD_0_0" type="text" label="v" value="" optional="True" argument="v" help=""/>
|
|
|
4834 </when>
|
|
|
4835 </conditional>
|
|
|
4836 <conditional name="CONDITIONAL_no_input_missing_phenotype">
|
|
|
4837 <param name="CONDITIONAL_SELECT_no_input_missing_phenotype" type="select" label="Set No input missing phenotype" help="Don't treat any nonzero number as a missing pheno/covar. ('NA'/'nan' are still treated as missing.) " argument="--no-input-missing-phenotype">
|
|
|
4838 <option value="no_set" selected="True">Don't set</option>
|
|
|
4839 <option value="set">Set value(s)</option>
|
|
|
4840 </param>
|
|
|
4841 <when value="no_set">
|
|
|
4842 </when>
|
|
|
4843 <when value="set">
|
|
|
4844
|
|
|
4845 </when>
|
|
|
4846 </conditional>
|
|
|
4847 <conditional name="CONDITIONAL_GALAXY_1">
|
|
|
4848 <param name="CONDITIONAL_SELECT_GALAXY_1" type="select" label="Set 1" help="Expect case/control phenotypes in input files to be coded as 0 = control, 1 = case, instead of the usual 0 = missing, 1 = ctrl, 2 = case. (Unlike PLINK 1.x, this does not force all phenotypes to be interpreted as case/ctrl.) " argument="--1">
|
|
|
4849 <option value="no_set" selected="True">Don't set</option>
|
|
|
4850 <option value="set">Set value(s)</option>
|
|
|
4851 </param>
|
|
|
4852 <when value="no_set">
|
|
|
4853 </when>
|
|
|
4854 <when value="set">
|
|
|
4855
|
|
|
4856 </when>
|
|
|
4857 </conditional>
|
|
|
4858 <conditional name="CONDITIONAL_missing_catname">
|
|
|
4859 <param name="CONDITIONAL_SELECT_missing_catname" type="select" label="Set Missing catname" help="Set missing-categorical-phenotype string (case-sensitive, default 'NONE'). " argument="--missing-catname">
|
|
|
4860 <option value="no_set" selected="True">Don't set</option>
|
|
|
4861 <option value="set">Set value(s)</option>
|
|
|
4862 </param>
|
|
|
4863 <when value="no_set">
|
|
|
4864 </when>
|
|
|
4865 <when value="set">
|
|
|
4866
|
|
|
4867 <param name="missing_catname_MOD_0_0" type="text" label="str" value="" optional="True" argument="str" help=""/>
|
|
|
4868 </when>
|
|
|
4869 </conditional>
|
|
|
4870 <conditional name="CONDITIONAL_covar">
|
|
|
4871 <param name="CONDITIONAL_SELECT_covar" type="select" label="Set Covar" help="Specify additional covariate file. Comma-delimited files with a header line are now permitted. " argument="--covar">
|
|
|
4872 <option value="no_set" selected="True">Don't set</option>
|
|
|
4873 <option value="set">Set value(s)</option>
|
|
|
4874 </param>
|
|
|
4875 <when value="no_set">
|
|
|
4876 </when>
|
|
|
4877 <when value="set">
|
|
|
4878
|
|
|
4879 <param name="covar_MOD_0_0" type="text" label="'iid-only'" value="" optional="False" argument="'iid-only'" help=""/>
|
|
|
4880 <param name="covar_MOD_1_0" type="data" format="plink.covar" label="f" multiple="False" optional="True" argument="f"/>
|
|
|
4881 </when>
|
|
|
4882 </conditional>
|
|
|
4883 <conditional name="CONDITIONAL_covar_name">
|
|
|
4884 <param name="CONDITIONAL_SELECT_covar_name" type="select" label="Set Covar name" help="Only load the designated covariate(s) from the --covar (if one was specified), --pheno (if no --covar), or .psam (if no --covar or --pheno) file. " argument="--covar-name">
|
|
|
4885 <option value="no_set" selected="True">Don't set</option>
|
|
|
4886 <option value="set">Set value(s)</option>
|
|
|
4887 </param>
|
|
|
4888 <when value="no_set">
|
|
|
4889 </when>
|
|
|
4890 <when value="set">
|
|
|
4891
|
|
|
4892 <param name="covar_name_MOD_0_0" type="text" label="name..." value="" optional="True" argument="name..." help="Multiple values are allowed"/>
|
|
|
4893 </when>
|
|
|
4894 </conditional>
|
|
|
4895 <conditional name="CONDITIONAL_covar_col_nums">
|
|
|
4896 <param name="CONDITIONAL_SELECT_covar_col_nums" type="select" label="Set Covar col nums" help="Only load the covariate(s) in the designated column number(s) from the --covar (if one was specified) or --pheno (if no --covar) file. " argument="--covar-col-nums">
|
|
|
4897 <option value="no_set" selected="True">Don't set</option>
|
|
|
4898 <option value="set">Set value(s)</option>
|
|
|
4899 </param>
|
|
|
4900 <when value="no_set">
|
|
|
4901 </when>
|
|
|
4902 <when value="set">
|
|
|
4903
|
|
|
4904 <param name="covar_col_nums_MOD_0_0" type="text" label="#..." value="" optional="True" argument="#..." help="Multiple values are allowed"/>
|
|
|
4905 </when>
|
|
|
4906 </conditional>
|
|
|
4907 <conditional name="CONDITIONAL_within">
|
|
|
4908 <param name="CONDITIONAL_SELECT_within" type="select" label="Set Within" help="Import a PLINK 1.x categorical phenotype. (Phenotype name defaults to 'CATPHENO'.) * If any numeric values are present, ALL values must be numeric. In that case, 'C' is added in front of all category names. * 'NA' is treated as a missing value. " argument="--within">
|
|
|
4909 <option value="no_set" selected="True">Don't set</option>
|
|
|
4910 <option value="set">Set value(s)</option>
|
|
|
4911 </param>
|
|
|
4912 <when value="no_set">
|
|
|
4913 </when>
|
|
|
4914 <when value="set">
|
|
|
4915
|
|
|
4916 <param name="within_MOD_0_0" type="data" format="tabular" label="f" multiple="False" optional="True" argument="f"/>
|
|
|
4917 <param name="within_MOD_1_0" type="text" label="new pheno name" value="" optional="False" argument="new pheno name" help=""/>
|
|
|
4918 </when>
|
|
|
4919 </conditional>
|
|
|
4920 <conditional name="CONDITIONAL_mwithin">
|
|
|
4921 <param name="CONDITIONAL_SELECT_mwithin" type="select" label="Set Mwithin" help="Load --within categories from column n+2. " argument="--mwithin">
|
|
|
4922 <option value="no_set" selected="True">Don't set</option>
|
|
|
4923 <option value="set">Set value(s)</option>
|
|
|
4924 </param>
|
|
|
4925 <when value="no_set">
|
|
|
4926 </when>
|
|
|
4927 <when value="set">
|
|
|
4928
|
|
|
4929 <param name="mwithin_MOD_0_0" type="integer" label="n" value="" optional="True" argument="n" help=""/>
|
|
|
4930 </when>
|
|
|
4931 </conditional>
|
|
|
4932 <conditional name="CONDITIONAL_family">
|
|
|
4933 <param name="CONDITIONAL_SELECT_family" type="select" label="Set Family" help="Create a categorical phenotype from FID. Restrictions on and handling of numeric values are the same as for --within. " argument="--family">
|
|
|
4934 <option value="no_set" selected="True">Don't set</option>
|
|
|
4935 <option value="set">Set value(s)</option>
|
|
|
4936 </param>
|
|
|
4937 <when value="no_set">
|
|
|
4938 </when>
|
|
|
4939 <when value="set">
|
|
|
4940
|
|
|
4941 <param name="family_MOD_0_0" type="text" label="new pheno name" value="" optional="False" argument="new pheno name" help=""/>
|
|
|
4942 </when>
|
|
|
4943 </conditional>
|
|
|
4944 <conditional name="CONDITIONAL_family_missing_catname">
|
|
|
4945 <param name="CONDITIONAL_SELECT_family_missing_catname" type="select" label="Set Family missing catname" help="Make --family treat the specified FID as missing. " argument="--family-missing-catname">
|
|
|
4946 <option value="no_set" selected="True">Don't set</option>
|
|
|
4947 <option value="set">Set value(s)</option>
|
|
|
4948 </param>
|
|
|
4949 <when value="no_set">
|
|
|
4950 </when>
|
|
|
4951 <when value="set">
|
|
|
4952
|
|
|
4953 <param name="family_missing_catname_MOD_0_0" type="text" label="nm" value="" optional="True" argument="nm" help=""/>
|
|
|
4954 </when>
|
|
|
4955 </conditional>
|
|
|
4956 <conditional name="CONDITIONAL_keep">
|
|
|
4957 <param name="CONDITIONAL_SELECT_keep" type="select" label="Set Keep" help="Exclude all samples not named in a file. " argument="--keep">
|
|
|
4958 <option value="no_set" selected="True">Don't set</option>
|
|
|
4959 <option value="set">Set value(s)</option>
|
|
|
4960 </param>
|
|
|
4961 <when value="no_set">
|
|
|
4962 </when>
|
|
|
4963 <when value="set">
|
|
|
4964
|
|
|
4965 <param name="keep_MOD_0_0" type="text" label="fname..." value="" optional="True" argument="fname..." help="Multiple values are allowed"/>
|
|
|
4966 </when>
|
|
|
4967 </conditional>
|
|
|
4968 <conditional name="CONDITIONAL_remove">
|
|
|
4969 <param name="CONDITIONAL_SELECT_remove" type="select" label="Set Remove" help="Exclude all samples named in a file. " argument="--remove">
|
|
|
4970 <option value="no_set" selected="True">Don't set</option>
|
|
|
4971 <option value="set">Set value(s)</option>
|
|
|
4972 </param>
|
|
|
4973 <when value="no_set">
|
|
|
4974 </when>
|
|
|
4975 <when value="set">
|
|
|
4976
|
|
|
4977 <param name="remove_MOD_0_0" type="text" label="fname..." value="" optional="True" argument="fname..." help="Multiple values are allowed"/>
|
|
|
4978 </when>
|
|
|
4979 </conditional>
|
|
|
4980 <conditional name="CONDITIONAL_keep_fam">
|
|
|
4981 <param name="CONDITIONAL_SELECT_keep_fam" type="select" label="Set Keep fam" help="Exclude all families not named in a file. " argument="--keep-fam">
|
|
|
4982 <option value="no_set" selected="True">Don't set</option>
|
|
|
4983 <option value="set">Set value(s)</option>
|
|
|
4984 </param>
|
|
|
4985 <when value="no_set">
|
|
|
4986 </when>
|
|
|
4987 <when value="set">
|
|
|
4988
|
|
|
4989 <param name="keep_fam_MOD_0_0" type="text" label="fn..." value="" optional="True" argument="fn..." help="Multiple values are allowed"/>
|
|
|
4990 </when>
|
|
|
4991 </conditional>
|
|
|
4992 <conditional name="CONDITIONAL_remove_fam">
|
|
|
4993 <param name="CONDITIONAL_SELECT_remove_fam" type="select" label="Set Remove fam" help="Exclude all families named in a file. " argument="--remove-fam">
|
|
|
4994 <option value="no_set" selected="True">Don't set</option>
|
|
|
4995 <option value="set">Set value(s)</option>
|
|
|
4996 </param>
|
|
|
4997 <when value="no_set">
|
|
|
4998 </when>
|
|
|
4999 <when value="set">
|
|
|
5000
|
|
|
5001 <param name="remove_fam_MOD_0_0" type="text" label="f..." value="" optional="True" argument="f..." help="Multiple values are allowed"/>
|
|
|
5002 </when>
|
|
|
5003 </conditional>
|
|
|
5004 <conditional name="CONDITIONAL_extract">
|
|
|
5005 <param name="CONDITIONAL_SELECT_extract" type="select" label="Set Extract" help="Usually excludes all variants (not) named " argument="--extract">
|
|
|
5006 <option value="no_set" selected="True">Don't set</option>
|
|
|
5007 <option value="set">Set value(s)</option>
|
|
|
5008 </param>
|
|
|
5009 <when value="no_set">
|
|
|
5010 </when>
|
|
|
5011 <when value="set">
|
|
|
5012
|
|
|
5013 <conditional name="CONDITIONAL_extract_MOD_0">
|
|
|
5014 <param name="CONDITIONAL_SELECT_extract_MOD_0" type="select" label="How to set Extract">
|
|
|
5015 <option value="no_set" selected="True">Don't set</option>
|
|
|
5016 <option value="from_list">Select from list</option>
|
|
|
5017
|
|
|
5018 </param>
|
|
|
5019 <when value="no_set">
|
|
|
5020 </when>
|
|
|
5021
|
|
|
5022 <when value="from_list">
|
|
|
5023 <param name="extract_MOD_0" type="select" label="Select value">
|
|
1
|
5024 <option value="{bed0"><![CDATA[{bed0]]></option>
|
|
|
5025 <option value="bed1}"><![CDATA[bed1}]]></option>
|
|
0
|
5026 </param>
|
|
|
5027 </when>
|
|
|
5028 </conditional>
|
|
|
5029 <param name="extract_MOD_1_0" type="text" label="f..." value="" optional="True" argument="f..." help="Multiple values are allowed"/>
|
|
|
5030 </when>
|
|
|
5031 </conditional>
|
|
|
5032 <conditional name="CONDITIONAL_exclude">
|
|
|
5033 <param name="CONDITIONAL_SELECT_exclude" type="select" label="Set Exclude" help="" argument="--exclude">
|
|
|
5034 <option value="no_set" selected="True">Don't set</option>
|
|
|
5035 <option value="set">Set value(s)</option>
|
|
|
5036 </param>
|
|
|
5037 <when value="no_set">
|
|
|
5038 </when>
|
|
|
5039 <when value="set">
|
|
|
5040
|
|
|
5041 <conditional name="CONDITIONAL_exclude_MOD_0">
|
|
|
5042 <param name="CONDITIONAL_SELECT_exclude_MOD_0" type="select" label="How to set Exclude">
|
|
|
5043 <option value="no_set" selected="True">Don't set</option>
|
|
|
5044 <option value="from_list">Select from list</option>
|
|
|
5045
|
|
|
5046 </param>
|
|
|
5047 <when value="no_set">
|
|
|
5048 </when>
|
|
|
5049
|
|
|
5050 <when value="from_list">
|
|
|
5051 <param name="exclude_MOD_0" type="select" label="Select value">
|
|
1
|
5052 <option value="{bed0"><![CDATA[{bed0]]></option>
|
|
|
5053 <option value="bed1}"><![CDATA[bed1}]]></option>
|
|
0
|
5054 </param>
|
|
|
5055 </when>
|
|
|
5056 </conditional>
|
|
|
5057 <param name="exclude_MOD_1_0" type="text" label="f..." value="" optional="True" argument="f..." help="Multiple values are allowed"/>
|
|
|
5058 </when>
|
|
|
5059 </conditional>
|
|
|
5060 <conditional name="CONDITIONAL_extract_intersect">
|
|
|
5061 <param name="CONDITIONAL_SELECT_extract_intersect" type="select" label="Set Extract intersect" help="Just like --extract, except that a variant must be in the intersection, rather than just the union, of the files to remain. " argument="--extract-intersect">
|
|
|
5062 <option value="no_set" selected="True">Don't set</option>
|
|
|
5063 <option value="set">Set value(s)</option>
|
|
|
5064 </param>
|
|
|
5065 <when value="no_set">
|
|
|
5066 </when>
|
|
|
5067 <when value="set">
|
|
|
5068
|
|
|
5069 <conditional name="CONDITIONAL_extract_intersect_MOD_0">
|
|
|
5070 <param name="CONDITIONAL_SELECT_extract_intersect_MOD_0" type="select" label="How to set Extract intersect">
|
|
|
5071 <option value="no_set" selected="True">Don't set</option>
|
|
|
5072 <option value="from_list">Select from list</option>
|
|
|
5073
|
|
|
5074 </param>
|
|
|
5075 <when value="no_set">
|
|
|
5076 </when>
|
|
|
5077
|
|
|
5078 <when value="from_list">
|
|
|
5079 <param name="extract_intersect_MOD_0" type="select" label="Select value">
|
|
1
|
5080 <option value="{bed0"><![CDATA[{bed0]]></option>
|
|
|
5081 <option value="bed1}"><![CDATA[bed1}]]></option>
|
|
0
|
5082 </param>
|
|
|
5083 </when>
|
|
|
5084 </conditional>
|
|
|
5085 <param name="extract_intersect_MOD_1_0" type="text" label="f..." value="" optional="True" argument="f..." help="Multiple values are allowed"/>
|
|
|
5086 </when>
|
|
|
5087 </conditional>
|
|
|
5088 <conditional name="CONDITIONAL_keep_cats">
|
|
|
5089 <param name="CONDITIONAL_SELECT_keep_cats" type="select" label="Set Keep cats" help="These can be used individually or in combination " argument="--keep-cats">
|
|
|
5090 <option value="no_set" selected="True">Don't set</option>
|
|
|
5091 <option value="set">Set value(s)</option>
|
|
|
5092 </param>
|
|
|
5093 <when value="no_set">
|
|
|
5094 </when>
|
|
|
5095 <when value="set">
|
|
|
5096
|
|
|
5097 <param name="keep_cats_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
5098 </when>
|
|
|
5099 </conditional>
|
|
|
5100 <conditional name="CONDITIONAL_keep_cat_names">
|
|
|
5101 <param name="CONDITIONAL_SELECT_keep_cat_names" type="select" label="Set Keep cat names" help="" argument="--keep-cat-names">
|
|
|
5102 <option value="no_set" selected="True">Don't set</option>
|
|
|
5103 <option value="set">Set value(s)</option>
|
|
|
5104 </param>
|
|
|
5105 <when value="no_set">
|
|
|
5106 </when>
|
|
|
5107 <when value="set">
|
|
|
5108
|
|
|
5109 <param name="keep_cat_names_MOD_0_0" type="text" label="nm..." value="" optional="True" argument="nm..." help="Multiple values are allowed"/>
|
|
|
5110 </when>
|
|
|
5111 </conditional>
|
|
|
5112 <conditional name="CONDITIONAL_keep_cat_pheno">
|
|
|
5113 <param name="CONDITIONAL_SELECT_keep_cat_pheno" type="select" label="Set Keep cat pheno" help="If more than one categorical phenotype is loaded, or you wish to filter on a categorical covariate, --keep-cat-pheno must be used to specify which phenotype/covariate --keep-cats and --keep-cat-names apply to. " argument="--keep-cat-pheno">
|
|
|
5114 <option value="no_set" selected="True">Don't set</option>
|
|
|
5115 <option value="set">Set value(s)</option>
|
|
|
5116 </param>
|
|
|
5117 <when value="no_set">
|
|
|
5118 </when>
|
|
|
5119 <when value="set">
|
|
|
5120
|
|
|
5121 <param name="keep_cat_pheno_MOD_0_0" type="text" label="pheno" value="" optional="True" argument="pheno" help=""/>
|
|
|
5122 </when>
|
|
|
5123 </conditional>
|
|
|
5124 <conditional name="CONDITIONAL_remove_cats">
|
|
|
5125 <param name="CONDITIONAL_SELECT_remove_cats" type="select" label="Set Remove cats" help="Exclude all categories named in the file. " argument="--remove-cats">
|
|
|
5126 <option value="no_set" selected="True">Don't set</option>
|
|
|
5127 <option value="set">Set value(s)</option>
|
|
|
5128 </param>
|
|
|
5129 <when value="no_set">
|
|
|
5130 </when>
|
|
|
5131 <when value="set">
|
|
|
5132
|
|
|
5133 <param name="remove_cats_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
5134 </when>
|
|
|
5135 </conditional>
|
|
|
5136 <conditional name="CONDITIONAL_remove_cat_names">
|
|
|
5137 <param name="CONDITIONAL_SELECT_remove_cat_names" type="select" label="Set Remove cat names" help="Exclude named categories. " argument="--remove-cat-names">
|
|
|
5138 <option value="no_set" selected="True">Don't set</option>
|
|
|
5139 <option value="set">Set value(s)</option>
|
|
|
5140 </param>
|
|
|
5141 <when value="no_set">
|
|
|
5142 </when>
|
|
|
5143 <when value="set">
|
|
|
5144
|
|
|
5145 <param name="remove_cat_names_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
|
|
|
5146 </when>
|
|
|
5147 </conditional>
|
|
|
5148 <conditional name="CONDITIONAL_remove_cat_pheno">
|
|
|
5149 <param name="CONDITIONAL_SELECT_remove_cat_pheno" type="select" label="Set Remove cat pheno" help="Specify pheno for --remove-cats/remove-cat-names. " argument="--remove-cat-pheno">
|
|
|
5150 <option value="no_set" selected="True">Don't set</option>
|
|
|
5151 <option value="set">Set value(s)</option>
|
|
|
5152 </param>
|
|
|
5153 <when value="no_set">
|
|
|
5154 </when>
|
|
|
5155 <when value="set">
|
|
|
5156
|
|
|
5157 <param name="remove_cat_pheno_MOD_0_0" type="text" label="phe" value="" optional="True" argument="phe" help=""/>
|
|
|
5158 </when>
|
|
|
5159 </conditional>
|
|
|
5160 <conditional name="CONDITIONAL_split_cat_pheno">
|
|
|
5161 <param name="CONDITIONAL_SELECT_split_cat_pheno" type="select" label="Set Split cat pheno" help="Split n-category phenotype(s) into n (or n-1, with 'omit-most'/'omit-last') binary phenotypes, with names of the form <orig. pheno name>=<cat. name>. (As a consequence, affected phenotypes and categories are not permitted to contain the '=' character.) * This happens after all sample filters. * If no phenotype or covariate names are provided, all categorical phenotypes (but not covariates) are processed. * By default, generated covariates are coded as 1=false, 2=true. To code them as 0=false, 1=true instead, add the 'covar-01' modifier." argument="--split-cat-pheno">
|
|
|
5162 <option value="no_set" selected="True">Don't set</option>
|
|
|
5163 <option value="set">Set value(s)</option>
|
|
|
5164 </param>
|
|
|
5165 <when value="no_set">
|
|
|
5166 </when>
|
|
|
5167 <when value="set">
|
|
|
5168
|
|
|
5169 <conditional name="CONDITIONAL_split_cat_pheno_MOD_0">
|
|
|
5170 <param name="CONDITIONAL_SELECT_split_cat_pheno_MOD_0" type="select" label="How to set Split cat pheno">
|
|
|
5171 <option value="no_set" selected="True">Don't set</option>
|
|
|
5172 <option value="from_list">Select from list</option>
|
|
|
5173
|
|
|
5174 </param>
|
|
|
5175 <when value="no_set">
|
|
|
5176 </when>
|
|
|
5177
|
|
|
5178 <when value="from_list">
|
|
|
5179 <param name="split_cat_pheno_MOD_0" type="select" label="Select value">
|
|
1
|
5180 <option value="{omit-most"><![CDATA[{omit-most]]></option>
|
|
|
5181 <option value="omit-last}"><![CDATA[omit-last}]]></option>
|
|
0
|
5182 </param>
|
|
|
5183 </when>
|
|
|
5184 </conditional>
|
|
|
5185 <param name="split_cat_pheno_MOD_1_0" type="text" label="'covar-01'" value="" optional="False" argument="'covar-01'" help=""/>
|
|
|
5186 <param name="split_cat_pheno_MOD_2_0" type="text" label="cat. pheno/covar name(s)..." value="" optional="False" argument="cat. pheno/covar name(s)..." help="Multiple values are allowed"/>
|
|
|
5187 </when>
|
|
|
5188 </conditional>
|
|
|
5189 <conditional name="CONDITIONAL_loop_cats">
|
|
|
5190 <param name="CONDITIONAL_SELECT_loop_cats" type="select" label="Set Loop cats" help="Run variant filters and subsequent operations on just the samples in the first category; then just the samples in the second category; and so on, for all categories in the named categorical phenotype. " argument="--loop-cats">
|
|
|
5191 <option value="no_set" selected="True">Don't set</option>
|
|
|
5192 <option value="set">Set value(s)</option>
|
|
|
5193 </param>
|
|
|
5194 <when value="no_set">
|
|
|
5195 </when>
|
|
|
5196 <when value="set">
|
|
|
5197
|
|
|
5198 <param name="loop_cats_MOD_0_0" type="text" label="pheno/covar" value="" optional="True" argument="pheno/covar" help=""/>
|
|
|
5199 </when>
|
|
|
5200 </conditional>
|
|
|
5201 <conditional name="CONDITIONAL_no_id_header">
|
|
|
5202 <param name="CONDITIONAL_SELECT_no_id_header" type="select" label="Set No id header" help="Don't include a header line in .id output files. This normally forces two-column FID/IID output; add 'iid-only' to force just single-column IID. " argument="--no-id-header">
|
|
|
5203 <option value="no_set" selected="True">Don't set</option>
|
|
|
5204 <option value="set">Set value(s)</option>
|
|
|
5205 </param>
|
|
|
5206 <when value="no_set">
|
|
|
5207 </when>
|
|
|
5208 <when value="set">
|
|
|
5209
|
|
|
5210 <param name="no_id_header_MOD_0_0" type="text" label="'iid-only'" value="" optional="False" argument="'iid-only'" help=""/>
|
|
|
5211 </when>
|
|
|
5212 </conditional>
|
|
|
5213 <conditional name="CONDITIONAL_variance_standardize">
|
|
|
5214 <param name="CONDITIONAL_SELECT_variance_standardize" type="select" label="Set Variance standardize" help="" argument="--variance-standardize">
|
|
|
5215 <option value="no_set" selected="True">Don't set</option>
|
|
|
5216 <option value="set">Set value(s)</option>
|
|
|
5217 </param>
|
|
|
5218 <when value="no_set">
|
|
|
5219 </when>
|
|
|
5220 <when value="set">
|
|
|
5221
|
|
|
5222 <param name="variance_standardize_MOD_0_0" type="text" label="pheno/covar name(s)..." value="" optional="False" argument="pheno/covar name(s)..." help="Multiple values are allowed"/>
|
|
|
5223 </when>
|
|
|
5224 </conditional>
|
|
|
5225 <conditional name="CONDITIONAL_covar_variance_standardize">
|
|
|
5226 <param name="CONDITIONAL_SELECT_covar_variance_standardize" type="select" label="Set Covar variance standardize" help="Linearly transform named covariates (and quantitative phenotypes, if --variance-standardize) to mean-zero, variance 1. If no parameters are provided, all possible phenotypes/covariates are affected. This is frequently necessary to prevent multicollinearity when dealing with covariates where abs(mean) is much larger than abs(standard deviation), such as year of birth." argument="--covar-variance-standardize">
|
|
|
5227 <option value="no_set" selected="True">Don't set</option>
|
|
|
5228 <option value="set">Set value(s)</option>
|
|
|
5229 </param>
|
|
|
5230 <when value="no_set">
|
|
|
5231 </when>
|
|
|
5232 <when value="set">
|
|
|
5233
|
|
|
5234 <param name="covar_variance_standardize_MOD_0_0" type="text" label="covar name(s)..." value="" optional="False" argument="covar name(s)..." help="Multiple values are allowed"/>
|
|
|
5235 </when>
|
|
|
5236 </conditional>
|
|
|
5237 <conditional name="CONDITIONAL_quantile_normalize">
|
|
|
5238 <param name="CONDITIONAL_SELECT_quantile_normalize" type="select" label="Set Quantile normalize" help="Force named covariates and quantitative " argument="--quantile-normalize">
|
|
|
5239 <option value="no_set" selected="True">Don't set</option>
|
|
|
5240 <option value="set">Set value(s)</option>
|
|
|
5241 </param>
|
|
|
5242 <when value="no_set">
|
|
|
5243 </when>
|
|
|
5244 <when value="set">
|
|
|
5245
|
|
|
5246 <param name="quantile_normalize_MOD_0_0" type="text" label="..." value="" optional="False" argument="..." help="Multiple values are allowed"/>
|
|
|
5247 </when>
|
|
|
5248 </conditional>
|
|
|
5249 <conditional name="CONDITIONAL_pheno_quantile_normalize">
|
|
|
5250 <param name="CONDITIONAL_SELECT_pheno_quantile_normalize" type="select" label="Set Pheno quantile normalize" help="" argument="--pheno-quantile-normalize">
|
|
|
5251 <option value="no_set" selected="True">Don't set</option>
|
|
|
5252 <option value="set">Set value(s)</option>
|
|
|
5253 </param>
|
|
|
5254 <when value="no_set">
|
|
|
5255 </when>
|
|
|
5256 <when value="set">
|
|
|
5257
|
|
|
5258 <param name="pheno_quantile_normalize_MOD_0_0" type="text" label="..." value="" optional="False" argument="..." help="Multiple values are allowed"/>
|
|
|
5259 </when>
|
|
|
5260 </conditional>
|
|
|
5261 <conditional name="CONDITIONAL_covar_quantile_normalize">
|
|
|
5262 <param name="CONDITIONAL_SELECT_covar_quantile_normalize" type="select" label="Set Covar quantile normalize" help="" argument="--covar-quantile-normalize">
|
|
|
5263 <option value="no_set" selected="True">Don't set</option>
|
|
|
5264 <option value="set">Set value(s)</option>
|
|
|
5265 </param>
|
|
|
5266 <when value="no_set">
|
|
|
5267 </when>
|
|
|
5268 <when value="set">
|
|
|
5269
|
|
|
5270 <param name="covar_quantile_normalize_MOD_0_0" type="text" label="..." value="" optional="False" argument="..." help="Multiple values are allowed"/>
|
|
|
5271 </when>
|
|
|
5272 </conditional>
|
|
|
5273 <conditional name="CONDITIONAL_chr">
|
|
|
5274 <param name="CONDITIONAL_SELECT_chr" type="select" label="Set Chr" help="Exclude all variants not on the given chromosome(s). Valid choices for humans are 0 (unplaced), 1-22, X, Y, XY, MT, PAR1, and PAR2. Separate multiple chromosomes with spaces and/or commas, and use a dash (no adjacent spaces permitted) to denote a range, e.g. '--chr 1-4, 22, par1, x, par2'. " argument="--chr">
|
|
|
5275 <option value="no_set" selected="True">Don't set</option>
|
|
|
5276 <option value="set">Set value(s)</option>
|
|
|
5277 </param>
|
|
|
5278 <when value="no_set">
|
|
|
5279 </when>
|
|
|
5280 <when value="set">
|
|
|
5281
|
|
|
5282 <param name="chr_MOD_0_0" type="text" label="chr(s)..." value="" optional="True" argument="chr(s)..." help="Multiple values are allowed"/>
|
|
|
5283 </when>
|
|
|
5284 </conditional>
|
|
|
5285 <conditional name="CONDITIONAL_not_chr">
|
|
|
5286 <param name="CONDITIONAL_SELECT_not_chr" type="select" label="Set Not chr" help="Reverse of --chr (exclude variants on listed chromosomes). " argument="--not-chr">
|
|
|
5287 <option value="no_set" selected="True">Don't set</option>
|
|
|
5288 <option value="set">Set value(s)</option>
|
|
|
5289 </param>
|
|
|
5290 <when value="no_set">
|
|
|
5291 </when>
|
|
|
5292 <when value="set">
|
|
|
5293
|
|
|
5294 <param name="not_chr_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
|
|
|
5295 </when>
|
|
|
5296 </conditional>
|
|
|
5297 <conditional name="CONDITIONAL_autosome">
|
|
|
5298 <param name="CONDITIONAL_SELECT_autosome" type="select" label="Set Autosome" help="Exclude all non-autosomal variants. " argument="--autosome">
|
|
|
5299 <option value="no_set" selected="True">Don't set</option>
|
|
|
5300 <option value="set">Set value(s)</option>
|
|
|
5301 </param>
|
|
|
5302 <when value="no_set">
|
|
|
5303 </when>
|
|
|
5304 <when value="set">
|
|
|
5305
|
|
|
5306 </when>
|
|
|
5307 </conditional>
|
|
|
5308 <conditional name="CONDITIONAL_autosome_par">
|
|
|
5309 <param name="CONDITIONAL_SELECT_autosome_par" type="select" label="Set Autosome par" help="Exclude all non-autosomal variants, except those in a pseudo-autosomal region. " argument="--autosome-par">
|
|
|
5310 <option value="no_set" selected="True">Don't set</option>
|
|
|
5311 <option value="set">Set value(s)</option>
|
|
|
5312 </param>
|
|
|
5313 <when value="no_set">
|
|
|
5314 </when>
|
|
|
5315 <when value="set">
|
|
|
5316
|
|
|
5317 </when>
|
|
|
5318 </conditional>
|
|
|
5319 <conditional name="CONDITIONAL_snps_only">
|
|
|
5320 <param name="CONDITIONAL_SELECT_snps_only" type="select" label="Set Snps only" help="Exclude non-SNP variants. By default, SNP = all allele codes are single-character (so multiallelic variants with a mix of SNPs and non-SNPs are excluded; split your variants first if that's a problem). The 'just-acgt' modifier restricts SNP codes to {A,C,G,T,a,c,g,t,<missing>}. " argument="--snps-only">
|
|
|
5321 <option value="no_set" selected="True">Don't set</option>
|
|
|
5322 <option value="set">Set value(s)</option>
|
|
|
5323 </param>
|
|
|
5324 <when value="no_set">
|
|
|
5325 </when>
|
|
|
5326 <when value="set">
|
|
|
5327
|
|
|
5328 <param name="snps_only_MOD_0_0" type="text" label="'just-acgt'" value="" optional="False" argument="'just-acgt'" help=""/>
|
|
|
5329 </when>
|
|
|
5330 </conditional>
|
|
|
5331 <conditional name="CONDITIONAL_from">
|
|
|
5332 <param name="CONDITIONAL_SELECT_from" type="select" label="Set From" help="Use ID(s) to specify a variant range to load. When used " argument="--from">
|
|
|
5333 <option value="no_set" selected="True">Don't set</option>
|
|
|
5334 <option value="set">Set value(s)</option>
|
|
|
5335 </param>
|
|
|
5336 <when value="no_set">
|
|
|
5337 </when>
|
|
|
5338 <when value="set">
|
|
|
5339
|
|
|
5340 <param name="from_MOD_0_0" type="text" label="var ID" value="" optional="True" argument="var ID" help=""/>
|
|
|
5341 </when>
|
|
|
5342 </conditional>
|
|
|
5343 <conditional name="CONDITIONAL_to">
|
|
|
5344 <param name="CONDITIONAL_SELECT_to" type="select" label="Set To" help="" argument="--to">
|
|
|
5345 <option value="no_set" selected="True">Don't set</option>
|
|
|
5346 <option value="set">Set value(s)</option>
|
|
|
5347 </param>
|
|
|
5348 <when value="no_set">
|
|
|
5349 </when>
|
|
|
5350 <when value="set">
|
|
|
5351
|
|
|
5352 <param name="to_MOD_0_0" type="text" label="var ID" value="" optional="True" argument="var ID" help=""/>
|
|
|
5353 </when>
|
|
|
5354 </conditional>
|
|
|
5355 <conditional name="CONDITIONAL_snp">
|
|
|
5356 <param name="CONDITIONAL_SELECT_snp" type="select" label="Set Snp" help="Specify a single variant to load. " argument="--snp">
|
|
|
5357 <option value="no_set" selected="True">Don't set</option>
|
|
|
5358 <option value="set">Set value(s)</option>
|
|
|
5359 </param>
|
|
|
5360 <when value="no_set">
|
|
|
5361 </when>
|
|
|
5362 <when value="set">
|
|
|
5363
|
|
|
5364 <param name="snp_MOD_0_0" type="text" label="var ID" value="" optional="True" argument="var ID" help=""/>
|
|
|
5365 </when>
|
|
|
5366 </conditional>
|
|
|
5367 <conditional name="CONDITIONAL_exclude_snp">
|
|
|
5368 <param name="CONDITIONAL_SELECT_exclude_snp" type="select" label="Set Exclude snp" help="Specify a single variant to exclude. " argument="--exclude-snp">
|
|
|
5369 <option value="no_set" selected="True">Don't set</option>
|
|
|
5370 <option value="set">Set value(s)</option>
|
|
|
5371 </param>
|
|
|
5372 <when value="no_set">
|
|
|
5373 </when>
|
|
|
5374 <when value="set">
|
|
|
5375
|
|
|
5376 <param name="exclude_snp_MOD_0_0" type="text" label="ID" value="" optional="True" argument="ID" help=""/>
|
|
|
5377 </when>
|
|
|
5378 </conditional>
|
|
|
5379 <conditional name="CONDITIONAL_window">
|
|
|
5380 <param name="CONDITIONAL_SELECT_window" type="select" label="Set Window" help="With --snp/--exclude-snp, loads/excludes all variants within half the specified kb distance of the named one. " argument="--window">
|
|
|
5381 <option value="no_set" selected="True">Don't set</option>
|
|
|
5382 <option value="set">Set value(s)</option>
|
|
|
5383 </param>
|
|
|
5384 <when value="no_set">
|
|
|
5385 </when>
|
|
|
5386 <when value="set">
|
|
|
5387
|
|
|
5388 <param name="window_MOD_0_0" type="text" label="kbs" value="" optional="True" argument="kbs" help=""/>
|
|
|
5389 </when>
|
|
|
5390 </conditional>
|
|
|
5391 <conditional name="CONDITIONAL_from_bp">
|
|
|
5392 <param name="CONDITIONAL_SELECT_from_bp" type="select" label="Set From bp" help="Use base-pair coordinates to define a variant range to " argument="--from-bp">
|
|
|
5393 <option value="no_set" selected="True">Don't set</option>
|
|
|
5394 <option value="set">Set value(s)</option>
|
|
|
5395 </param>
|
|
|
5396 <when value="no_set">
|
|
|
5397 </when>
|
|
|
5398 <when value="set">
|
|
|
5399
|
|
|
5400 <param name="from_bp_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/>
|
|
|
5401 </when>
|
|
|
5402 </conditional>
|
|
|
5403 <conditional name="CONDITIONAL_to_bp">
|
|
|
5404 <param name="CONDITIONAL_SELECT_to_bp" type="select" label="Set To bp" help="" argument="--to-bp">
|
|
|
5405 <option value="no_set" selected="True">Don't set</option>
|
|
|
5406 <option value="set">Set value(s)</option>
|
|
|
5407 </param>
|
|
|
5408 <when value="no_set">
|
|
|
5409 </when>
|
|
|
5410 <when value="set">
|
|
|
5411
|
|
|
5412 <param name="to_bp_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/>
|
|
|
5413 </when>
|
|
|
5414 </conditional>
|
|
|
5415 <conditional name="CONDITIONAL_from_kb">
|
|
|
5416 <param name="CONDITIONAL_SELECT_from_kb" type="select" label="Set From kb" help="" argument="--from-kb">
|
|
|
5417 <option value="no_set" selected="True">Don't set</option>
|
|
|
5418 <option value="set">Set value(s)</option>
|
|
|
5419 </param>
|
|
|
5420 <when value="no_set">
|
|
|
5421 </when>
|
|
|
5422 <when value="set">
|
|
|
5423
|
|
|
5424 <param name="from_kb_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/>
|
|
|
5425 </when>
|
|
|
5426 </conditional>
|
|
|
5427 <conditional name="CONDITIONAL_to_kb">
|
|
|
5428 <param name="CONDITIONAL_SELECT_to_kb" type="select" label="Set To kb" help="" argument="--to-kb">
|
|
|
5429 <option value="no_set" selected="True">Don't set</option>
|
|
|
5430 <option value="set">Set value(s)</option>
|
|
|
5431 </param>
|
|
|
5432 <when value="no_set">
|
|
|
5433 </when>
|
|
|
5434 <when value="set">
|
|
|
5435
|
|
|
5436 <param name="to_kb_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/>
|
|
|
5437 </when>
|
|
|
5438 </conditional>
|
|
|
5439 <conditional name="CONDITIONAL_from_mb">
|
|
|
5440 <param name="CONDITIONAL_SELECT_from_mb" type="select" label="Set From mb" help="" argument="--from-mb">
|
|
|
5441 <option value="no_set" selected="True">Don't set</option>
|
|
|
5442 <option value="set">Set value(s)</option>
|
|
|
5443 </param>
|
|
|
5444 <when value="no_set">
|
|
|
5445 </when>
|
|
|
5446 <when value="set">
|
|
|
5447
|
|
|
5448 <param name="from_mb_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/>
|
|
|
5449 </when>
|
|
|
5450 </conditional>
|
|
|
5451 <conditional name="CONDITIONAL_to_mb">
|
|
|
5452 <param name="CONDITIONAL_SELECT_to_mb" type="select" label="Set To mb" help="" argument="--to-mb">
|
|
|
5453 <option value="no_set" selected="True">Don't set</option>
|
|
|
5454 <option value="set">Set value(s)</option>
|
|
|
5455 </param>
|
|
|
5456 <when value="no_set">
|
|
|
5457 </when>
|
|
|
5458 <when value="set">
|
|
|
5459
|
|
|
5460 <param name="to_mb_MOD_0_0" type="text" label="pos" value="" optional="True" argument="pos" help=""/>
|
|
|
5461 </when>
|
|
|
5462 </conditional>
|
|
|
5463 <conditional name="CONDITIONAL_snps">
|
|
|
5464 <param name="CONDITIONAL_SELECT_snps" type="select" label="Set Snps" help="Use IDs to specify variant range(s) to load or " argument="--snps">
|
|
|
5465 <option value="no_set" selected="True">Don't set</option>
|
|
|
5466 <option value="set">Set value(s)</option>
|
|
|
5467 </param>
|
|
|
5468 <when value="no_set">
|
|
|
5469 </when>
|
|
|
5470 <when value="set">
|
|
|
5471
|
|
|
5472 <param name="snps_MOD_0_0" type="text" label="var IDs..." value="" optional="True" argument="var IDs..." help="Multiple values are allowed"/>
|
|
|
5473 </when>
|
|
|
5474 </conditional>
|
|
|
5475 <conditional name="CONDITIONAL_exclude_snps">
|
|
|
5476 <param name="CONDITIONAL_SELECT_exclude_snps" type="select" label="Set Exclude snps" help="" argument="--exclude-snps">
|
|
|
5477 <option value="no_set" selected="True">Don't set</option>
|
|
|
5478 <option value="set">Set value(s)</option>
|
|
|
5479 </param>
|
|
|
5480 <when value="no_set">
|
|
|
5481 </when>
|
|
|
5482 <when value="set">
|
|
|
5483
|
|
|
5484 <param name="exclude_snps_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
|
|
|
5485 </when>
|
|
|
5486 </conditional>
|
|
|
5487 <conditional name="CONDITIONAL_force_intersect">
|
|
|
5488 <param name="CONDITIONAL_SELECT_force_intersect" type="select" label="Set Force intersect" help="PLINK 2 normally errors out when multiple variant inclusion filters (--extract, --extract-col-cond, --extract-intersect, --from/--to, --from-bp/--to-bp, --snp, --snps) are specified. --force-intersect allows the run to proceed; the set intersection will be taken. " argument="--force-intersect">
|
|
|
5489 <option value="no_set" selected="True">Don't set</option>
|
|
|
5490 <option value="set">Set value(s)</option>
|
|
|
5491 </param>
|
|
|
5492 <when value="no_set">
|
|
|
5493 </when>
|
|
|
5494 <when value="set">
|
|
|
5495
|
|
|
5496 </when>
|
|
|
5497 </conditional>
|
|
|
5498 <conditional name="CONDITIONAL_thin">
|
|
|
5499 <param name="CONDITIONAL_SELECT_thin" type="select" label="Set Thin" help="Randomly remove variants, retaining each with prob. p. " argument="--thin">
|
|
|
5500 <option value="no_set" selected="True">Don't set</option>
|
|
|
5501 <option value="set">Set value(s)</option>
|
|
|
5502 </param>
|
|
|
5503 <when value="no_set">
|
|
|
5504 </when>
|
|
|
5505 <when value="set">
|
|
|
5506
|
|
|
5507 <param name="thin_MOD_0_0" type="float" label="p" value="" optional="True" argument="p" help=""/>
|
|
|
5508 </when>
|
|
|
5509 </conditional>
|
|
|
5510 <conditional name="CONDITIONAL_thin_count">
|
|
|
5511 <param name="CONDITIONAL_SELECT_thin_count" type="select" label="Set Thin count" help="Randomly remove variants until n of them remain. " argument="--thin-count">
|
|
|
5512 <option value="no_set" selected="True">Don't set</option>
|
|
|
5513 <option value="set">Set value(s)</option>
|
|
|
5514 </param>
|
|
|
5515 <when value="no_set">
|
|
|
5516 </when>
|
|
|
5517 <when value="set">
|
|
|
5518
|
|
|
5519 <param name="thin_count_MOD_0_0" type="integer" label="n" value="" optional="True" argument="n" help=""/>
|
|
|
5520 </when>
|
|
|
5521 </conditional>
|
|
|
5522 <conditional name="CONDITIONAL_bp_space">
|
|
|
5523 <param name="CONDITIONAL_SELECT_bp_space" type="select" label="Set Bp space" help="Remove variants so that each pair is no closer than the given bp distance. " argument="--bp-space">
|
|
|
5524 <option value="no_set" selected="True">Don't set</option>
|
|
|
5525 <option value="set">Set value(s)</option>
|
|
|
5526 </param>
|
|
|
5527 <when value="no_set">
|
|
|
5528 </when>
|
|
|
5529 <when value="set">
|
|
|
5530
|
|
|
5531 <param name="bp_space_MOD_0_0" type="text" label="bps" value="" optional="True" argument="bps" help=""/>
|
|
|
5532 </when>
|
|
|
5533 </conditional>
|
|
|
5534 <conditional name="CONDITIONAL_thin_indiv">
|
|
|
5535 <param name="CONDITIONAL_SELECT_thin_indiv" type="select" label="Set Thin indiv" help="Randomly remove samples, retaining with prob. p. " argument="--thin-indiv">
|
|
|
5536 <option value="no_set" selected="True">Don't set</option>
|
|
|
5537 <option value="set">Set value(s)</option>
|
|
|
5538 </param>
|
|
|
5539 <when value="no_set">
|
|
|
5540 </when>
|
|
|
5541 <when value="set">
|
|
|
5542
|
|
|
5543 <param name="thin_indiv_MOD_0_0" type="float" label="p" value="" optional="True" argument="p" help=""/>
|
|
|
5544 </when>
|
|
|
5545 </conditional>
|
|
|
5546 <conditional name="CONDITIONAL_thin_indiv_count">
|
|
|
5547 <param name="CONDITIONAL_SELECT_thin_indiv_count" type="select" label="Set Thin indiv count" help="Randomly remove samples until n of them remain. " argument="--thin-indiv-count">
|
|
|
5548 <option value="no_set" selected="True">Don't set</option>
|
|
|
5549 <option value="set">Set value(s)</option>
|
|
|
5550 </param>
|
|
|
5551 <when value="no_set">
|
|
|
5552 </when>
|
|
|
5553 <when value="set">
|
|
|
5554
|
|
|
5555 <param name="thin_indiv_count_MOD_0_0" type="integer" label="n" value="" optional="True" argument="n" help=""/>
|
|
|
5556 </when>
|
|
|
5557 </conditional>
|
|
|
5558 <conditional name="CONDITIONAL_keep_col_match">
|
|
|
5559 <param name="CONDITIONAL_SELECT_keep_col_match" type="select" label="Set Keep col match" help="Exclude all samples without a 3rd column entry in the given file exactly matching one of the given strings. (Separate multiple strings with spaces.) " argument="--keep-col-match">
|
|
|
5560 <option value="no_set" selected="True">Don't set</option>
|
|
|
5561 <option value="set">Set value(s)</option>
|
|
|
5562 </param>
|
|
|
5563 <when value="no_set">
|
|
|
5564 </when>
|
|
|
5565 <when value="set">
|
|
|
5566
|
|
|
5567 <param name="keep_col_match_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/>
|
|
|
5568 <param name="keep_col_match_MOD_1_0" type="text" label="val(s)..." value="" optional="True" argument="val(s)..." help="Multiple values are allowed"/>
|
|
|
5569 </when>
|
|
|
5570 </conditional>
|
|
|
5571 <conditional name="CONDITIONAL_keep_col_match_name">
|
|
|
5572 <param name="CONDITIONAL_SELECT_keep_col_match_name" type="select" label="Set Keep col match name" help="Check column with given name instead. " argument="--keep-col-match-name">
|
|
|
5573 <option value="no_set" selected="True">Don't set</option>
|
|
|
5574 <option value="set">Set value(s)</option>
|
|
|
5575 </param>
|
|
|
5576 <when value="no_set">
|
|
|
5577 </when>
|
|
|
5578 <when value="set">
|
|
|
5579
|
|
|
5580 <param name="keep_col_match_name_MOD_0_0" type="text" label="col name" value="" optional="True" argument="col name" help=""/>
|
|
|
5581 </when>
|
|
|
5582 </conditional>
|
|
|
5583 <conditional name="CONDITIONAL_keep_col_match_num">
|
|
|
5584 <param name="CONDITIONAL_SELECT_keep_col_match_num" type="select" label="Set Keep col match num" help="Check nth column instead. " argument="--keep-col-match-num">
|
|
|
5585 <option value="no_set" selected="True">Don't set</option>
|
|
|
5586 <option value="set">Set value(s)</option>
|
|
|
5587 </param>
|
|
|
5588 <when value="no_set">
|
|
|
5589 </when>
|
|
|
5590 <when value="set">
|
|
|
5591
|
|
|
5592 <param name="keep_col_match_num_MOD_0_0" type="integer" label="n" value="" optional="True" argument="n" help=""/>
|
|
|
5593 </when>
|
|
|
5594 </conditional>
|
|
|
5595 <conditional name="CONDITIONAL_geno">
|
|
|
5596 <param name="CONDITIONAL_SELECT_geno" type="select" label="Set Geno" help="" argument="--geno">
|
|
|
5597 <option value="no_set" selected="True">Don't set</option>
|
|
|
5598 <option value="set">Set value(s)</option>
|
|
|
5599 </param>
|
|
|
5600 <when value="no_set">
|
|
|
5601 </when>
|
|
|
5602 <when value="set">
|
|
|
5603
|
|
|
5604 <param name="geno_MOD_0_0" type="text" label="val" value="" optional="False" argument="val" help=""/>
|
|
|
5605 <conditional name="CONDITIONAL_geno_MOD_1">
|
|
|
5606 <param name="CONDITIONAL_SELECT_geno_MOD_1" type="select" label="How to set Geno">
|
|
|
5607 <option value="no_set" selected="True">Don't set</option>
|
|
|
5608 <option value="from_list">Select from list</option>
|
|
|
5609
|
|
|
5610 </param>
|
|
|
5611 <when value="no_set">
|
|
|
5612 </when>
|
|
|
5613
|
|
|
5614 <when value="from_list">
|
|
|
5615 <param name="geno_MOD_1" type="select" label="Select value">
|
|
1
|
5616 <option value="{dosage"><![CDATA[{dosage]]></option>
|
|
|
5617 <option value="hh-missing}"><![CDATA[hh-missing}]]></option>
|
|
0
|
5618 </param>
|
|
|
5619 </when>
|
|
|
5620 </conditional>
|
|
|
5621 </when>
|
|
|
5622 </conditional>
|
|
|
5623 <conditional name="CONDITIONAL_mind">
|
|
|
5624 <param name="CONDITIONAL_SELECT_mind" type="select" label="Set Mind" help="Exclude variants (--geno) and/or samples (--mind) with missing call frequencies greater than a threshold (default 0.1). (Note that the default threshold is only applied if --geno/--mind is invoked without a parameter; when --geno/--mind is not invoked, no missing call frequency ceiling is enforced at all. Other inclusion/exclusion default thresholds work the same way.) By default, when a dosage is present but a hardcall is not, the genotype is treated as missing; add the 'dosage' modifier to treat this case as nonmissing. Alternatively, you can use 'hh-missing' to also treat heterozygous haploid calls as missing." argument="--mind">
|
|
|
5625 <option value="no_set" selected="True">Don't set</option>
|
|
|
5626 <option value="set">Set value(s)</option>
|
|
|
5627 </param>
|
|
|
5628 <when value="no_set">
|
|
|
5629 </when>
|
|
|
5630 <when value="set">
|
|
|
5631
|
|
|
5632 <param name="mind_MOD_0_0" type="text" label="val" value="" optional="False" argument="val" help=""/>
|
|
|
5633 <conditional name="CONDITIONAL_mind_MOD_1">
|
|
|
5634 <param name="CONDITIONAL_SELECT_mind_MOD_1" type="select" label="How to set Mind">
|
|
|
5635 <option value="no_set" selected="True">Don't set</option>
|
|
|
5636 <option value="from_list">Select from list</option>
|
|
|
5637
|
|
|
5638 </param>
|
|
|
5639 <when value="no_set">
|
|
|
5640 </when>
|
|
|
5641
|
|
|
5642 <when value="from_list">
|
|
|
5643 <param name="mind_MOD_1" type="select" label="Select value">
|
|
1
|
5644 <option value="{dosage"><![CDATA[{dosage]]></option>
|
|
|
5645 <option value="hh-missing}"><![CDATA[hh-missing}]]></option>
|
|
0
|
5646 </param>
|
|
|
5647 </when>
|
|
|
5648 </conditional>
|
|
|
5649 </when>
|
|
|
5650 </conditional>
|
|
|
5651 <conditional name="CONDITIONAL_require_pheno">
|
|
|
5652 <param name="CONDITIONAL_SELECT_require_pheno" type="select" label="Set Require pheno" help="Remove samples missing any of the named " argument="--require-pheno">
|
|
|
5653 <option value="no_set" selected="True">Don't set</option>
|
|
|
5654 <option value="set">Set value(s)</option>
|
|
|
5655 </param>
|
|
|
5656 <when value="no_set">
|
|
|
5657 </when>
|
|
|
5658 <when value="set">
|
|
|
5659
|
|
|
5660 <param name="require_pheno_MOD_0_0" type="text" label="name(s)..." value="" optional="False" argument="name(s)..." help="Multiple values are allowed"/>
|
|
|
5661 </when>
|
|
|
5662 </conditional>
|
|
|
5663 <conditional name="CONDITIONAL_require_covar">
|
|
|
5664 <param name="CONDITIONAL_SELECT_require_covar" type="select" label="Set Require covar" help="" argument="--require-covar">
|
|
|
5665 <option value="no_set" selected="True">Don't set</option>
|
|
|
5666 <option value="set">Set value(s)</option>
|
|
|
5667 </param>
|
|
|
5668 <when value="no_set">
|
|
|
5669 </when>
|
|
|
5670 <when value="set">
|
|
|
5671
|
|
|
5672 <param name="require_covar_MOD_0_0" type="text" label="name(s)..." value="" optional="False" argument="name(s)..." help="Multiple values are allowed"/>
|
|
|
5673 </when>
|
|
|
5674 </conditional>
|
|
|
5675 <conditional name="CONDITIONAL_maf">
|
|
|
5676 <param name="CONDITIONAL_SELECT_maf" type="select" label="Set Maf" help="Exclude variants with allele frequency lower than a (alias: --min-af) threshold (default 0.01). By default, the nonmajor allele frequency is used; the other supported modes are 'nref' (non-reference), 'alt1', and 'minor' (least frequent). bcftools freq:mode notation is permitted." argument="--maf">
|
|
|
5677 <option value="no_set" selected="True">Don't set</option>
|
|
|
5678 <option value="set">Set value(s)</option>
|
|
|
5679 </param>
|
|
|
5680 <when value="no_set">
|
|
|
5681 </when>
|
|
|
5682 <when value="set">
|
|
|
5683
|
|
|
5684 <param name="maf_MOD_0_0" type="float" label="freq" value="" optional="False" argument="freq" help=""/>
|
|
|
5685 <param name="maf_MOD_1_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/>
|
|
|
5686 </when>
|
|
|
5687 </conditional>
|
|
|
5688 <conditional name="CONDITIONAL_max_maf">
|
|
|
5689 <param name="CONDITIONAL_SELECT_max_maf" type="select" label="Set Max maf" help="Exclude variants with MAF greater than the (alias: --max-af) threshold." argument="--max-maf">
|
|
|
5690 <option value="no_set" selected="True">Don't set</option>
|
|
|
5691 <option value="set">Set value(s)</option>
|
|
|
5692 </param>
|
|
|
5693 <when value="no_set">
|
|
|
5694 </when>
|
|
|
5695 <when value="set">
|
|
|
5696
|
|
|
5697 <param name="max_maf_MOD_0_0" type="float" label="freq" value="" optional="True" argument="freq" help=""/>
|
|
|
5698 <param name="max_maf_MOD_1_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/>
|
|
|
5699 </when>
|
|
|
5700 </conditional>
|
|
|
5701 <conditional name="CONDITIONAL_mac">
|
|
|
5702 <param name="CONDITIONAL_SELECT_mac" type="select" label="Set Mac" help="Exclude variants with allele dosage lower than the (alias: --min-ac) given threshold." argument="--mac">
|
|
|
5703 <option value="no_set" selected="True">Don't set</option>
|
|
|
5704 <option value="set">Set value(s)</option>
|
|
|
5705 </param>
|
|
|
5706 <when value="no_set">
|
|
|
5707 </when>
|
|
|
5708 <when value="set">
|
|
|
5709
|
|
|
5710 <param name="mac_MOD_0_0" type="integer" label="ct" value="" optional="True" argument="ct" help=""/>
|
|
|
5711 <param name="mac_MOD_1_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/>
|
|
|
5712 </when>
|
|
|
5713 </conditional>
|
|
|
5714 <conditional name="CONDITIONAL_max_mac">
|
|
|
5715 <param name="CONDITIONAL_SELECT_max_mac" type="select" label="Set Max mac" help="Exclude variants with allele dosage greater than (alias: --max-ac) the given threshold." argument="--max-mac">
|
|
|
5716 <option value="no_set" selected="True">Don't set</option>
|
|
|
5717 <option value="set">Set value(s)</option>
|
|
|
5718 </param>
|
|
|
5719 <when value="no_set">
|
|
|
5720 </when>
|
|
|
5721 <when value="set">
|
|
|
5722
|
|
|
5723 <param name="max_mac_MOD_0_0" type="integer" label="ct" value="" optional="True" argument="ct" help=""/>
|
|
|
5724 <param name="max_mac_MOD_1_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/>
|
|
|
5725 </when>
|
|
|
5726 </conditional>
|
|
|
5727 <conditional name="CONDITIONAL_maf_succ">
|
|
|
5728 <param name="CONDITIONAL_SELECT_maf_succ" type="select" label="Set Maf succ" help="Rule of succession allele frequency estimation (used in EIGENSOFT). Given j observations of one allele and k observations of the other for a biallelic variant, infer allele frequencies of (j+1) / (j+k+2) and (k+1) / (j+k+2), rather than the default j / (j+k) and k / (j+k). Note that this does not affect --freq's output. " argument="--maf-succ">
|
|
|
5729 <option value="no_set" selected="True">Don't set</option>
|
|
|
5730 <option value="set">Set value(s)</option>
|
|
|
5731 </param>
|
|
|
5732 <when value="no_set">
|
|
|
5733 </when>
|
|
|
5734 <when value="set">
|
|
|
5735
|
|
|
5736 </when>
|
|
|
5737 </conditional>
|
|
|
5738 <conditional name="CONDITIONAL_min_alleles">
|
|
|
5739 <param name="CONDITIONAL_SELECT_min_alleles" type="select" label="Set Min alleles" help="Exclude variants with fewer than the given # of alleles. (When a variant has exactly one ALT allele, and it's a missing-code, it's excluded by "--min-alleles 2".) " argument="--min-alleles">
|
|
|
5740 <option value="no_set" selected="True">Don't set</option>
|
|
|
5741 <option value="set">Set value(s)</option>
|
|
|
5742 </param>
|
|
|
5743 <when value="no_set">
|
|
|
5744 </when>
|
|
|
5745 <when value="set">
|
|
|
5746
|
|
|
5747 <param name="min_alleles_MOD_0_0" type="integer" label="ct" value="" optional="True" argument="ct" help=""/>
|
|
|
5748 </when>
|
|
|
5749 </conditional>
|
|
|
5750 <conditional name="CONDITIONAL_max_alleles">
|
|
|
5751 <param name="CONDITIONAL_SELECT_max_alleles" type="select" label="Set Max alleles" help="Exclude variants with more than the given # of alleles. " argument="--max-alleles">
|
|
|
5752 <option value="no_set" selected="True">Don't set</option>
|
|
|
5753 <option value="set">Set value(s)</option>
|
|
|
5754 </param>
|
|
|
5755 <when value="no_set">
|
|
|
5756 </when>
|
|
|
5757 <when value="set">
|
|
|
5758
|
|
|
5759 <param name="max_alleles_MOD_0_0" type="integer" label="ct" value="" optional="True" argument="ct" help=""/>
|
|
|
5760 </when>
|
|
|
5761 </conditional>
|
|
|
5762 <conditional name="CONDITIONAL_read_freq">
|
|
|
5763 <param name="CONDITIONAL_SELECT_read_freq" type="select" label="Set Read freq" help="Load allele frequency estimates from the given --freq or --geno-counts (or PLINK 1.9 --freqx) report, instead of imputing them from the immediate dataset. " argument="--read-freq">
|
|
|
5764 <option value="no_set" selected="True">Don't set</option>
|
|
|
5765 <option value="set">Set value(s)</option>
|
|
|
5766 </param>
|
|
|
5767 <when value="no_set">
|
|
|
5768 </when>
|
|
|
5769 <when value="set">
|
|
|
5770
|
|
|
5771 <param name="read_freq_MOD_0_0" type="text" label="file" value="" optional="True" argument="file" help=""/>
|
|
|
5772 </when>
|
|
|
5773 </conditional>
|
|
|
5774 <conditional name="CONDITIONAL_hwe">
|
|
|
5775 <param name="CONDITIONAL_SELECT_hwe" type="select" label="Set Hwe" help="Exclude variants with Hardy-Weinberg equilibrium exact test p-values below a threshold. * By default, only founders are considered. * chrX p-values are now computed using Graffelman and Weir's method. * For variants with k alleles with k>2, k separate 'biallelic' tests are performed, and the variant is filtered out if any of them fail. * With 'keep-fewhet', variants which fail the test in the too-few-hets direction are not excluded. On chrX, this uses the ratio between the Graffelman/Weir p-value and the female-only p-value. * There is currently no special handling of case/control phenotypes." argument="--hwe">
|
|
|
5776 <option value="no_set" selected="True">Don't set</option>
|
|
|
5777 <option value="set">Set value(s)</option>
|
|
|
5778 </param>
|
|
|
5779 <when value="no_set">
|
|
|
5780 </when>
|
|
|
5781 <when value="set">
|
|
|
5782
|
|
|
5783 <param name="hwe_MOD_0_0" type="float" label="p" value="" optional="True" argument="p" help=""/>
|
|
|
5784 <param name="hwe_MOD_1_0" type="text" label="'midp'" value="" optional="False" argument="'midp'" help=""/>
|
|
|
5785 <param name="hwe_MOD_2_0" type="text" label="'keep-fewhet'" value="" optional="False" argument="'keep-fewhet'" help=""/>
|
|
|
5786 </when>
|
|
|
5787 </conditional>
|
|
|
5788 <conditional name="CONDITIONAL_mach_r2_filter">
|
|
|
5789 <param name="CONDITIONAL_SELECT_mach_r2_filter" type="select" label="Set Mach r2 filter" help="Exclude variants with MaCH imputation quality metric less than min or greater than max (defaults 0.1 and 2.0). (Monomorphic variants, with r2 = nan, are not excluded.) * This is NOT identical to the R2 metric reported by Minimac3 0.1.13+; see below. * If a single parameter is provided, it is treated as the minimum. * The metric is not computed on chrX and MT. " argument="--mach-r2-filter">
|
|
|
5790 <option value="no_set" selected="True">Don't set</option>
|
|
|
5791 <option value="set">Set value(s)</option>
|
|
|
5792 </param>
|
|
|
5793 <when value="no_set">
|
|
|
5794 </when>
|
|
|
5795 <when value="set">
|
|
|
5796
|
|
|
5797 <param name="mach_r2_filter_MOD_0_0" type="text" label="min" value="" optional="False" argument="min" help=""/>
|
|
|
5798 <param name="mach_r2_filter_MOD_1_0" type="text" label="max" value="" optional="False" argument="max" help=""/>
|
|
|
5799 </when>
|
|
|
5800 </conditional>
|
|
|
5801 <conditional name="CONDITIONAL_minimac3_r2_filter">
|
|
|
5802 <param name="CONDITIONAL_SELECT_minimac3_r2_filter" type="select" label="Set Minimac3 r2 filter" help="Compute Minimac3 R2 values from scratch, and exclude variants with R2 less than min or (if max is provided) greater than max. * Note that this requires phased-dosage data for all samples and variants; otherwise this will systematically underestimate imputation quality, since unphased hardcalls/dosages are treated as if they were maximally uncertain. (Use --extract-if-info/--exclude-if-info to filter on precomputed Minimac3 R2 in a VCF/.pvar INFO column.) " argument="--minimac3-r2-filter">
|
|
|
5803 <option value="no_set" selected="True">Don't set</option>
|
|
|
5804 <option value="set">Set value(s)</option>
|
|
|
5805 </param>
|
|
|
5806 <when value="no_set">
|
|
|
5807 </when>
|
|
|
5808 <when value="set">
|
|
|
5809
|
|
|
5810 <param name="minimac3_r2_filter_MOD_0_0" type="text" label="min" value="" optional="True" argument="min" help=""/>
|
|
|
5811 <param name="minimac3_r2_filter_MOD_1_0" type="text" label="max" value="" optional="False" argument="max" help=""/>
|
|
|
5812 </when>
|
|
|
5813 </conditional>
|
|
|
5814 <conditional name="CONDITIONAL_keep_females">
|
|
|
5815 <param name="CONDITIONAL_SELECT_keep_females" type="select" label="Set Keep females" help="Exclude male and unknown-sex samples. " argument="--keep-females">
|
|
|
5816 <option value="no_set" selected="True">Don't set</option>
|
|
|
5817 <option value="set">Set value(s)</option>
|
|
|
5818 </param>
|
|
|
5819 <when value="no_set">
|
|
|
5820 </when>
|
|
|
5821 <when value="set">
|
|
|
5822
|
|
|
5823 </when>
|
|
|
5824 </conditional>
|
|
|
5825 <conditional name="CONDITIONAL_keep_males">
|
|
|
5826 <param name="CONDITIONAL_SELECT_keep_males" type="select" label="Set Keep males" help="Exclude female and unknown-sex samples. " argument="--keep-males">
|
|
|
5827 <option value="no_set" selected="True">Don't set</option>
|
|
|
5828 <option value="set">Set value(s)</option>
|
|
|
5829 </param>
|
|
|
5830 <when value="no_set">
|
|
|
5831 </when>
|
|
|
5832 <when value="set">
|
|
|
5833
|
|
|
5834 </when>
|
|
|
5835 </conditional>
|
|
|
5836 <conditional name="CONDITIONAL_keep_nosex">
|
|
|
5837 <param name="CONDITIONAL_SELECT_keep_nosex" type="select" label="Set Keep nosex" help="Exclude all known-sex samples. " argument="--keep-nosex">
|
|
|
5838 <option value="no_set" selected="True">Don't set</option>
|
|
|
5839 <option value="set">Set value(s)</option>
|
|
|
5840 </param>
|
|
|
5841 <when value="no_set">
|
|
|
5842 </when>
|
|
|
5843 <when value="set">
|
|
|
5844
|
|
|
5845 </when>
|
|
|
5846 </conditional>
|
|
|
5847 <conditional name="CONDITIONAL_remove_females">
|
|
|
5848 <param name="CONDITIONAL_SELECT_remove_females" type="select" label="Set Remove females" help="Exclude female samples. " argument="--remove-females">
|
|
|
5849 <option value="no_set" selected="True">Don't set</option>
|
|
|
5850 <option value="set">Set value(s)</option>
|
|
|
5851 </param>
|
|
|
5852 <when value="no_set">
|
|
|
5853 </when>
|
|
|
5854 <when value="set">
|
|
|
5855
|
|
|
5856 </when>
|
|
|
5857 </conditional>
|
|
|
5858 <conditional name="CONDITIONAL_remove_males">
|
|
|
5859 <param name="CONDITIONAL_SELECT_remove_males" type="select" label="Set Remove males" help="Exclude male samples. " argument="--remove-males">
|
|
|
5860 <option value="no_set" selected="True">Don't set</option>
|
|
|
5861 <option value="set">Set value(s)</option>
|
|
|
5862 </param>
|
|
|
5863 <when value="no_set">
|
|
|
5864 </when>
|
|
|
5865 <when value="set">
|
|
|
5866
|
|
|
5867 </when>
|
|
|
5868 </conditional>
|
|
|
5869 <conditional name="CONDITIONAL_remove_nosex">
|
|
|
5870 <param name="CONDITIONAL_SELECT_remove_nosex" type="select" label="Set Remove nosex" help="Exclude unknown-sex samples. " argument="--remove-nosex">
|
|
|
5871 <option value="no_set" selected="True">Don't set</option>
|
|
|
5872 <option value="set">Set value(s)</option>
|
|
|
5873 </param>
|
|
|
5874 <when value="no_set">
|
|
|
5875 </when>
|
|
|
5876 <when value="set">
|
|
|
5877
|
|
|
5878 </when>
|
|
|
5879 </conditional>
|
|
|
5880 <conditional name="CONDITIONAL_keep_founders">
|
|
|
5881 <param name="CONDITIONAL_SELECT_keep_founders" type="select" label="Set Keep founders" help="Exclude nonfounder samples. " argument="--keep-founders">
|
|
|
5882 <option value="no_set" selected="True">Don't set</option>
|
|
|
5883 <option value="set">Set value(s)</option>
|
|
|
5884 </param>
|
|
|
5885 <when value="no_set">
|
|
|
5886 </when>
|
|
|
5887 <when value="set">
|
|
|
5888
|
|
|
5889 </when>
|
|
|
5890 </conditional>
|
|
|
5891 <conditional name="CONDITIONAL_keep_nonfounders">
|
|
|
5892 <param name="CONDITIONAL_SELECT_keep_nonfounders" type="select" label="Set Keep nonfounders" help="Exclude founder samples. " argument="--keep-nonfounders">
|
|
|
5893 <option value="no_set" selected="True">Don't set</option>
|
|
|
5894 <option value="set">Set value(s)</option>
|
|
|
5895 </param>
|
|
|
5896 <when value="no_set">
|
|
|
5897 </when>
|
|
|
5898 <when value="set">
|
|
|
5899
|
|
|
5900 </when>
|
|
|
5901 </conditional>
|
|
|
5902 <conditional name="CONDITIONAL_keep_if">
|
|
|
5903 <param name="CONDITIONAL_SELECT_keep_if" type="select" label="Set Keep if" help="Exclude samples which don't/do satisfy a " argument="--keep-if">
|
|
|
5904 <option value="no_set" selected="True">Don't set</option>
|
|
|
5905 <option value="set">Set value(s)</option>
|
|
|
5906 </param>
|
|
|
5907 <when value="no_set">
|
|
|
5908 </when>
|
|
|
5909 <when value="set">
|
|
|
5910
|
|
|
5911 <param name="keep_if_MOD_0_0" type="text" label="pheno/covar" value="" optional="True" argument="pheno/covar" help=""/>
|
|
|
5912 <param name="keep_if_MOD_1_0" type="text" label="op" value="" optional="True" argument="op" help=""/>
|
|
|
5913 <param name="keep_if_MOD_2_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
5914 </when>
|
|
|
5915 </conditional>
|
|
|
5916 <conditional name="CONDITIONAL_remove_if">
|
|
|
5917 <param name="CONDITIONAL_SELECT_remove_if" type="select" label="Set Remove if" help="" argument="--remove-if">
|
|
|
5918 <option value="no_set" selected="True">Don't set</option>
|
|
|
5919 <option value="set">Set value(s)</option>
|
|
|
5920 </param>
|
|
|
5921 <when value="no_set">
|
|
|
5922 </when>
|
|
|
5923 <when value="set">
|
|
|
5924
|
|
|
5925 <param name="remove_if_MOD_0_0" type="text" label="pheno/covar" value="" optional="True" argument="pheno/covar" help=""/>
|
|
|
5926 <param name="remove_if_MOD_1_0" type="text" label="op" value="" optional="True" argument="op" help=""/>
|
|
|
5927 <param name="remove_if_MOD_2_0" type="text" label="v" value="" optional="True" argument="v" help=""/>
|
|
|
5928 </when>
|
|
|
5929 </conditional>
|
|
|
5930 <conditional name="CONDITIONAL_nonfounders">
|
|
|
5931 <param name="CONDITIONAL_SELECT_nonfounders" type="select" label="Set Nonfounders" help="Include nonfounders in allele freq/HWE calculations. " argument="--nonfounders">
|
|
|
5932 <option value="no_set" selected="True">Don't set</option>
|
|
|
5933 <option value="set">Set value(s)</option>
|
|
|
5934 </param>
|
|
|
5935 <when value="no_set">
|
|
|
5936 </when>
|
|
|
5937 <when value="set">
|
|
|
5938
|
|
|
5939 </when>
|
|
|
5940 </conditional>
|
|
|
5941 <conditional name="CONDITIONAL_bad_freqs">
|
|
|
5942 <param name="CONDITIONAL_SELECT_bad_freqs" type="select" label="Set Bad freqs" help="When PLINK 2 needs decent allele frequencies, it normally errors out if they aren't provided by --read-freq and less than 50 founders are available to impute them from. Use --bad-freqs to force PLINK 2 to proceed in this case. " argument="--bad-freqs">
|
|
|
5943 <option value="no_set" selected="True">Don't set</option>
|
|
|
5944 <option value="set">Set value(s)</option>
|
|
|
5945 </param>
|
|
|
5946 <when value="no_set">
|
|
|
5947 </when>
|
|
|
5948 <when value="set">
|
|
|
5949
|
|
|
5950 </when>
|
|
|
5951 </conditional>
|
|
|
5952 <conditional name="CONDITIONAL_export_allele">
|
|
|
5953 <param name="CONDITIONAL_SELECT_export_allele" type="select" label="Set Export allele" help="With --export A/A-transpose/AD, count alleles named in the file, instead of REF alleles. " argument="--export-allele">
|
|
|
5954 <option value="no_set" selected="True">Don't set</option>
|
|
|
5955 <option value="set">Set value(s)</option>
|
|
|
5956 </param>
|
|
|
5957 <when value="no_set">
|
|
|
5958 </when>
|
|
|
5959 <when value="set">
|
|
|
5960
|
|
|
5961 <param name="export_allele_MOD_0_0" type="text" label="file" value="" optional="True" argument="file" help=""/>
|
|
|
5962 </when>
|
|
|
5963 </conditional>
|
|
|
5964 <conditional name="CONDITIONAL_output_chr">
|
|
|
5965 <param name="CONDITIONAL_SELECT_output_chr" type="select" label="Set Output chr" help="Set chromosome coding scheme in output files by providing the desired human mitochondrial code. Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM', and 'chrMT'; default is now 'MT' (note that this is a change from PLINK 1.x, which defaulted to '26'). " argument="--output-chr">
|
|
|
5966 <option value="no_set" selected="True">Don't set</option>
|
|
|
5967 <option value="set">Set value(s)</option>
|
|
|
5968 </param>
|
|
|
5969 <when value="no_set">
|
|
|
5970 </when>
|
|
|
5971 <when value="set">
|
|
|
5972
|
|
|
5973 <param name="output_chr_MOD_0_0" type="text" label="MT code" value="" optional="True" argument="MT code" help=""/>
|
|
|
5974 </when>
|
|
|
5975 </conditional>
|
|
|
5976 <conditional name="CONDITIONAL_output_missing_genotype">
|
|
|
5977 <param name="CONDITIONAL_SELECT_output_missing_genotype" type="select" label="Set Output missing genotype" help="Set the code used to represent missing genotypes in output files (default '.'). " argument="--output-missing-genotype">
|
|
|
5978 <option value="no_set" selected="True">Don't set</option>
|
|
|
5979 <option value="set">Set value(s)</option>
|
|
|
5980 </param>
|
|
|
5981 <when value="no_set">
|
|
|
5982 </when>
|
|
|
5983 <when value="set">
|
|
|
5984
|
|
|
5985 <param name="output_missing_genotype_MOD_0_0" type="text" label="ch" value="" optional="True" argument="ch" help=""/>
|
|
|
5986 </when>
|
|
|
5987 </conditional>
|
|
|
5988 <conditional name="CONDITIONAL_output_missing_phenotype">
|
|
|
5989 <param name="CONDITIONAL_SELECT_output_missing_phenotype" type="select" label="Set Output missing phenotype" help="Set the string used to represent missing phenotypes in output files (default 'NA'). " argument="--output-missing-phenotype">
|
|
|
5990 <option value="no_set" selected="True">Don't set</option>
|
|
|
5991 <option value="set">Set value(s)</option>
|
|
|
5992 </param>
|
|
|
5993 <when value="no_set">
|
|
|
5994 </when>
|
|
|
5995 <when value="set">
|
|
|
5996
|
|
|
5997 <param name="output_missing_phenotype_MOD_0_0" type="text" label="s" value="" optional="True" argument="s" help=""/>
|
|
|
5998 </when>
|
|
|
5999 </conditional>
|
|
|
6000 <conditional name="CONDITIONAL_sort_vars">
|
|
|
6001 <param name="CONDITIONAL_SELECT_sort_vars" type="select" label="Set Sort vars" help="Sort variants by chromosome, then position, then ID. The following string orders are supported: * 'natural'/'n': Natural sort (default). * 'ascii'/'a': ASCII. This must be used with --make-[b]pgen/--make-bed. " argument="--sort-vars">
|
|
|
6002 <option value="no_set" selected="True">Don't set</option>
|
|
|
6003 <option value="set">Set value(s)</option>
|
|
|
6004 </param>
|
|
|
6005 <when value="no_set">
|
|
|
6006 </when>
|
|
|
6007 <when value="set">
|
|
|
6008
|
|
|
6009 <param name="sort_vars_MOD_0_0" type="text" label="mode" value="" optional="False" argument="mode" help=""/>
|
|
|
6010 </when>
|
|
|
6011 </conditional>
|
|
|
6012 <conditional name="CONDITIONAL_set_hh_missing">
|
|
|
6013 <param name="CONDITIONAL_SELECT_set_hh_missing" type="select" label="Set Set hh missing" help="Make --make-[b]pgen/--make-bed set non-MT heterozygous haploid hardcalls, and all female chrY calls, to missing. (Unlike PLINK 1.x, this treats unknown-sex chrY genotypes like males, not females.) By default, all associated dosages are also erased; use 'keep-dosage' to keep them all. " argument="--set-hh-missing">
|
|
|
6014 <option value="no_set" selected="True">Don't set</option>
|
|
|
6015 <option value="set">Set value(s)</option>
|
|
|
6016 </param>
|
|
|
6017 <when value="no_set">
|
|
|
6018 </when>
|
|
|
6019 <when value="set">
|
|
|
6020
|
|
|
6021 <param name="set_hh_missing_MOD_0_0" type="text" label="'keep-dosage'" value="" optional="False" argument="'keep-dosage'" help=""/>
|
|
|
6022 </when>
|
|
|
6023 </conditional>
|
|
|
6024 <conditional name="CONDITIONAL_set_mixed_mt_missing">
|
|
|
6025 <param name="CONDITIONAL_SELECT_set_mixed_mt_missing" type="select" label="Set Set mixed mt missing" help="Make --make-[b]pgen/--make-bed set mixed MT hardcalls to missing. " argument="--set-mixed-mt-missing">
|
|
|
6026 <option value="no_set" selected="True">Don't set</option>
|
|
|
6027 <option value="set">Set value(s)</option>
|
|
|
6028 </param>
|
|
|
6029 <when value="no_set">
|
|
|
6030 </when>
|
|
|
6031 <when value="set">
|
|
|
6032
|
|
|
6033 <param name="set_mixed_mt_missing_MOD_0_0" type="text" label="'keep-dosage'" value="" optional="False" argument="'keep-dosage'" help=""/>
|
|
|
6034 </when>
|
|
|
6035 </conditional>
|
|
|
6036 <conditional name="CONDITIONAL_OVERLOADED_split_par">
|
|
|
6037 <param name="CONDITIONAL_OVERLOADED_SELECT_split_par" type="select" label="Choose argument form for Split_par" help="Overloaded argument, must chose a form">
|
|
|
6038 <option value="form_0">Form 0</option>
|
|
|
6039 <option value="form_1">Form 1</option>
|
|
|
6040 </param>
|
|
|
6041 <when value="form_0">
|
|
|
6042
|
|
|
6043 <conditional name="CONDITIONAL_split_par">
|
|
|
6044 <param name="CONDITIONAL_SELECT_split_par" type="select" label="Set Split par" help="Changes chromosome code of all X chromosome " argument="--split-par">
|
|
|
6045 <option value="no_set" selected="True">Don't set</option>
|
|
|
6046 <option value="set">Set value(s)</option>
|
|
|
6047 </param>
|
|
|
6048 <when value="no_set">
|
|
|
6049 </when>
|
|
|
6050 <when value="set">
|
|
|
6051
|
|
|
6052 <param name="split_par_MOD_0_0" type="text" label="bp1" value="" optional="True" argument="bp1" help=""/>
|
|
|
6053 <param name="split_par_MOD_1_0" type="text" label="bp2" value="" optional="True" argument="bp2" help=""/>
|
|
|
6054 </when>
|
|
|
6055 </conditional>
|
|
|
6056 </when>
|
|
|
6057 <when value="form_1">
|
|
|
6058
|
|
|
6059 <conditional name="CONDITIONAL_split_par">
|
|
|
6060 <param name="CONDITIONAL_SELECT_split_par" type="select" label="Set Split par" help="* 'b36'/'hg18' = NCBI 36, 2709521/154584237 * 'b37'/'hg19' = GRCh37, 2699520/154931044 * 'b38'/'hg38' = GRCh38, 2781479/155701383 " argument="--split-par">
|
|
|
6061 <option value="no_set" selected="True">Don't set</option>
|
|
|
6062 <option value="set">Set value(s)</option>
|
|
|
6063 </param>
|
|
|
6064 <when value="no_set">
|
|
|
6065 </when>
|
|
|
6066 <when value="set">
|
|
|
6067
|
|
|
6068 <param name="split_par_MOD_0_0" type="text" label="build" value="" optional="True" argument="build" help=""/>
|
|
|
6069 <param name="split_par_MOD_1_0" type="text" label="= bp1 to PAR1, and those with position" value="" optional="True" argument="= bp1 to PAR1, and those with position" help=""/>
|
|
|
6070 </when>
|
|
|
6071 </conditional>
|
|
|
6072 </when>
|
|
|
6073 </conditional>
|
|
|
6074 <conditional name="CONDITIONAL_merge_par">
|
|
|
6075 <param name="CONDITIONAL_SELECT_merge_par" type="select" label="Set Merge par" help='Merge PAR1/PAR2 back with X. Requires PAR1 to be positioned immediately before X, and PAR2 to be immediately after X. (Should *not* be used with "--export vcf", since it causes male homozygous/missing calls in PAR1/PAR2 to be reported as haploid.) ' argument="--merge-par">
|
|
|
6076 <option value="no_set" selected="True">Don't set</option>
|
|
|
6077 <option value="set">Set value(s)</option>
|
|
|
6078 </param>
|
|
|
6079 <when value="no_set">
|
|
|
6080 </when>
|
|
|
6081 <when value="set">
|
|
|
6082
|
|
|
6083 </when>
|
|
|
6084 </conditional>
|
|
|
6085 <conditional name="CONDITIONAL_merge_x">
|
|
|
6086 <param name="CONDITIONAL_SELECT_merge_x" type="select" label="Set Merge x" help="Merge XY back with X. This usually has to be combined with --sort-vars. " argument="--merge-x">
|
|
|
6087 <option value="no_set" selected="True">Don't set</option>
|
|
|
6088 <option value="set">Set value(s)</option>
|
|
|
6089 </param>
|
|
|
6090 <when value="no_set">
|
|
|
6091 </when>
|
|
|
6092 <when value="set">
|
|
|
6093
|
|
|
6094 </when>
|
|
|
6095 </conditional>
|
|
|
6096 <conditional name="CONDITIONAL_set_missing_var_ids">
|
|
|
6097 <param name="CONDITIONAL_SELECT_set_missing_var_ids" type="select" label="Set Set missing var ids" help="Given a template string with a '@' where the " argument="--set-missing-var-ids">
|
|
|
6098 <option value="no_set" selected="True">Don't set</option>
|
|
|
6099 <option value="set">Set value(s)</option>
|
|
|
6100 </param>
|
|
|
6101 <when value="no_set">
|
|
|
6102 </when>
|
|
|
6103 <when value="set">
|
|
|
6104
|
|
|
6105 <param name="set_missing_var_ids_MOD_0_0" type="text" label="t" value="" optional="True" argument="t" help=""/>
|
|
|
6106 </when>
|
|
|
6107 </conditional>
|
|
|
6108 <conditional name="CONDITIONAL_set_all_var_ids">
|
|
|
6109 <param name="CONDITIONAL_SELECT_set_all_var_ids" type="select" label="Set Set all var ids" help="" argument="--set-all-var-ids">
|
|
|
6110 <option value="no_set" selected="True">Don't set</option>
|
|
|
6111 <option value="set">Set value(s)</option>
|
|
|
6112 </param>
|
|
|
6113 <when value="no_set">
|
|
|
6114 </when>
|
|
|
6115 <when value="set">
|
|
|
6116
|
|
|
6117 <param name="set_all_var_ids_MOD_0_0" type="text" label="t" value="" optional="True" argument="t" help=""/>
|
|
|
6118 </when>
|
|
|
6119 </conditional>
|
|
|
6120 <conditional name="CONDITIONAL_var_id_multi">
|
|
|
6121 <param name="CONDITIONAL_SELECT_var_id_multi" type="select" label="Set Var id multi" help="Specify alternative templates for multiallelic " argument="--var-id-multi">
|
|
|
6122 <option value="no_set" selected="True">Don't set</option>
|
|
|
6123 <option value="set">Set value(s)</option>
|
|
|
6124 </param>
|
|
|
6125 <when value="no_set">
|
|
|
6126 </when>
|
|
|
6127 <when value="set">
|
|
|
6128
|
|
|
6129 <param name="var_id_multi_MOD_0_0" type="text" label="t" value="" optional="True" argument="t" help=""/>
|
|
|
6130 </when>
|
|
|
6131 </conditional>
|
|
|
6132 <conditional name="CONDITIONAL_var_id_multi_nonsnp">
|
|
|
6133 <param name="CONDITIONAL_SELECT_var_id_multi_nonsnp" type="select" label="Set Var id multi nonsnp" help="" argument="--var-id-multi-nonsnp">
|
|
|
6134 <option value="no_set" selected="True">Don't set</option>
|
|
|
6135 <option value="set">Set value(s)</option>
|
|
|
6136 </param>
|
|
|
6137 <when value="no_set">
|
|
|
6138 </when>
|
|
|
6139 <when value="set">
|
|
|
6140
|
|
|
6141 <param name="var_id_multi_nonsnp_MOD_0_0" type="text" label="t" value="" optional="True" argument="t" help=""/>
|
|
|
6142 </when>
|
|
|
6143 </conditional>
|
|
|
6144 <conditional name="CONDITIONAL_new_id_max_allele_len">
|
|
|
6145 <param name="CONDITIONAL_SELECT_new_id_max_allele_len" type="select" label="Set New id max allele len" help="Specify maximum number of leading characters from allele codes to include in new variant IDs, and behavior on longer codes (defaults 23, error)." argument="--new-id-max-allele-len">
|
|
|
6146 <option value="no_set" selected="True">Don't set</option>
|
|
|
6147 <option value="set">Set value(s)</option>
|
|
|
6148 </param>
|
|
|
6149 <when value="no_set">
|
|
|
6150 </when>
|
|
|
6151 <when value="set">
|
|
|
6152
|
|
|
6153 <param name="new_id_max_allele_len_MOD_0_0" type="text" label="len" value="" optional="True" argument="len" help=""/>
|
|
|
6154 <conditional name="CONDITIONAL_new_id_max_allele_len_MOD_1">
|
|
|
6155 <param name="CONDITIONAL_SELECT_new_id_max_allele_len_MOD_1" type="select" label="How to set New id max allele len">
|
|
|
6156 <option value="no_set" selected="True">Don't set</option>
|
|
|
6157 <option value="from_list">Select from list</option>
|
|
|
6158
|
|
|
6159 </param>
|
|
|
6160 <when value="no_set">
|
|
|
6161 </when>
|
|
|
6162
|
|
|
6163 <when value="from_list">
|
|
|
6164 <param name="new_id_max_allele_len_MOD_1" type="select" label="Select value">
|
|
1
|
6165 <option value="{error"><![CDATA[{error]]></option>
|
|
|
6166 <option value="missing"><![CDATA[missing]]></option>
|
|
|
6167 <option value="truncate}"><![CDATA[truncate}]]></option>
|
|
0
|
6168 </param>
|
|
|
6169 </when>
|
|
|
6170 </conditional>
|
|
|
6171 </when>
|
|
|
6172 </conditional>
|
|
|
6173 <conditional name="CONDITIONAL_missing_var_code">
|
|
|
6174 <param name="CONDITIONAL_SELECT_missing_var_code" type="select" label="Set Missing var code" help="Change unnamed variant code for --rm-dup, --set-{missing|all}-var-ids, and --recover-var-ids (default '.'). " argument="--missing-var-code">
|
|
|
6175 <option value="no_set" selected="True">Don't set</option>
|
|
|
6176 <option value="set">Set value(s)</option>
|
|
|
6177 </param>
|
|
|
6178 <when value="no_set">
|
|
|
6179 </when>
|
|
|
6180 <when value="set">
|
|
|
6181
|
|
|
6182 <param name="missing_var_code_MOD_0_0" type="text" label="str" value="" optional="True" argument="str" help=""/>
|
|
|
6183 </when>
|
|
|
6184 </conditional>
|
|
|
6185 <conditional name="CONDITIONAL_update_map">
|
|
|
6186 <param name="CONDITIONAL_SELECT_update_map" type="select" label="Set Update map" help="Update variant bp positions. " argument="--update-map">
|
|
|
6187 <option value="no_set" selected="True">Don't set</option>
|
|
|
6188 <option value="set">Set value(s)</option>
|
|
|
6189 </param>
|
|
|
6190 <when value="no_set">
|
|
|
6191 </when>
|
|
|
6192 <when value="set">
|
|
|
6193
|
|
|
6194 <param name="update_map_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/>
|
|
|
6195 <param name="update_map_MOD_1_0" type="text" label="bpcol" value="" optional="False" argument="bpcol" help=""/>
|
|
|
6196 <param name="update_map_MOD_2_0" type="text" label="IDcol" value="" optional="False" argument="IDcol" help=""/>
|
|
|
6197 <param name="update_map_MOD_3_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/>
|
|
|
6198 </when>
|
|
|
6199 </conditional>
|
|
|
6200 <conditional name="CONDITIONAL_update_name">
|
|
|
6201 <param name="CONDITIONAL_SELECT_update_name" type="select" label="Set Update name" help="Update variant IDs. " argument="--update-name">
|
|
|
6202 <option value="no_set" selected="True">Don't set</option>
|
|
|
6203 <option value="set">Set value(s)</option>
|
|
|
6204 </param>
|
|
|
6205 <when value="no_set">
|
|
|
6206 </when>
|
|
|
6207 <when value="set">
|
|
|
6208
|
|
|
6209 <param name="update_name_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/>
|
|
|
6210 <param name="update_name_MOD_1_0" type="text" label="newcol" value="" optional="False" argument="newcol" help=""/>
|
|
|
6211 <param name="update_name_MOD_2_0" type="text" label="oldcol" value="" optional="False" argument="oldcol" help=""/>
|
|
|
6212 <param name="update_name_MOD_3_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/>
|
|
|
6213 </when>
|
|
|
6214 </conditional>
|
|
|
6215 <conditional name="CONDITIONAL_recover_var_ids">
|
|
|
6216 <param name="CONDITIONAL_SELECT_recover_var_ids" type="select" label="Set Recover var ids" help="Undo --set-all-var-ids, given the original .pvar/VCF/.bim file. Original IDs are looked up by position and allele codes. * By default, if the original-ID file is a .bim, allele order is ignored. Use 'strict-bim-order' to force A1=ALT, A2=REF. * If any variant has multiple matching records in the original-ID file, and the IDs conflict, --recover-var-ids writes the affected (current) ID(s) to <output prefix>.recoverid.dup, and normally errors out. If the original-ID file has the same number of variants in the same order, you can still recover the old IDs with the 'rigid' modifier in this case. Alternatively, to proceed and assign the missing-ID code to these variants, add the 'force' modifier. (The .recoverid.dup file is still written when 'rigid' or 'force' is specified.) * --recover-var-ids normally expects to replace all variant IDs, and errors out if any are left untouched. Add the 'partial' modifier when you actually want to update just a proper subset." argument="--recover-var-ids">
|
|
|
6217 <option value="no_set" selected="True">Don't set</option>
|
|
|
6218 <option value="set">Set value(s)</option>
|
|
|
6219 </param>
|
|
|
6220 <when value="no_set">
|
|
|
6221 </when>
|
|
|
6222 <when value="set">
|
|
|
6223
|
|
|
6224 <param name="recover_var_ids_MOD_0_0" type="text" label="file" value="" optional="True" argument="file" help=""/>
|
|
|
6225 <param name="recover_var_ids_MOD_1_0" type="text" label="'strict-bim-order'" value="" optional="False" argument="'strict-bim-order'" help=""/>
|
|
|
6226 <conditional name="CONDITIONAL_recover_var_ids_MOD_2">
|
|
|
6227 <param name="CONDITIONAL_SELECT_recover_var_ids_MOD_2" type="select" label="How to set Recover var ids">
|
|
|
6228 <option value="no_set" selected="True">Don't set</option>
|
|
|
6229 <option value="from_list">Select from list</option>
|
|
|
6230
|
|
|
6231 </param>
|
|
|
6232 <when value="no_set">
|
|
|
6233 </when>
|
|
|
6234
|
|
|
6235 <when value="from_list">
|
|
|
6236 <param name="recover_var_ids_MOD_2" type="select" label="Select value">
|
|
1
|
6237 <option value="{rigid"><![CDATA[{rigid]]></option>
|
|
|
6238 <option value="force}"><![CDATA[force}]]></option>
|
|
0
|
6239 </param>
|
|
|
6240 </when>
|
|
|
6241 </conditional>
|
|
|
6242 <param name="recover_var_ids_MOD_3_0" type="text" label="'partial'" value="" optional="False" argument="'partial'" help=""/>
|
|
|
6243 </when>
|
|
|
6244 </conditional>
|
|
|
6245 <conditional name="CONDITIONAL_update_alleles">
|
|
|
6246 <param name="CONDITIONAL_SELECT_update_alleles" type="select" label="Set Update alleles" help="Update variant allele codes. " argument="--update-alleles">
|
|
|
6247 <option value="no_set" selected="True">Don't set</option>
|
|
|
6248 <option value="set">Set value(s)</option>
|
|
|
6249 </param>
|
|
|
6250 <when value="no_set">
|
|
|
6251 </when>
|
|
|
6252 <when value="set">
|
|
|
6253
|
|
|
6254 <param name="update_alleles_MOD_0_0" type="data" format="txt" label="fname" multiple="False" optional="True" argument="fname"/>
|
|
|
6255 </when>
|
|
|
6256 </conditional>
|
|
|
6257 <conditional name="CONDITIONAL_update_ids">
|
|
|
6258 <param name="CONDITIONAL_SELECT_update_ids" type="select" label="Set Update ids" help="Update sample IDs. " argument="--update-ids">
|
|
|
6259 <option value="no_set" selected="True">Don't set</option>
|
|
|
6260 <option value="set">Set value(s)</option>
|
|
|
6261 </param>
|
|
|
6262 <when value="no_set">
|
|
|
6263 </when>
|
|
|
6264 <when value="set">
|
|
|
6265
|
|
|
6266 <param name="update_ids_MOD_0_0" type="data" format="txt" label="fname" multiple="False" optional="True" argument="fname"/>
|
|
|
6267 </when>
|
|
|
6268 </conditional>
|
|
|
6269 <conditional name="CONDITIONAL_update_parents">
|
|
|
6270 <param name="CONDITIONAL_SELECT_update_parents" type="select" label="Set Update parents" help="Update parental IDs. " argument="--update-parents">
|
|
|
6271 <option value="no_set" selected="True">Don't set</option>
|
|
|
6272 <option value="set">Set value(s)</option>
|
|
|
6273 </param>
|
|
|
6274 <when value="no_set">
|
|
|
6275 </when>
|
|
|
6276 <when value="set">
|
|
|
6277
|
|
|
6278 <param name="update_parents_MOD_0_0" type="data" format="txt" label="fname" multiple="False" optional="True" argument="fname"/>
|
|
|
6279 </when>
|
|
|
6280 </conditional>
|
|
|
6281 <conditional name="CONDITIONAL_update_sex">
|
|
|
6282 <param name="CONDITIONAL_SELECT_update_sex" type="select" label="Set Update sex" help="Update sex information. * By default, if there is a header line starting with '#FID'/'#IID', sex is loaded from the first column titled 'SEX' (any capitalization); otherwise, column 3 is assumed. Use 'col-num=' to force a column number. * Only the first character in the sex column is processed. By default, '1'/'M'/'m' is interpreted as male, '2'/'F'/'f' is interpreted as female, and '0'/'N' is interpreted as unknown-sex. To change this to '0'/'M'/'m' = male, '1'/'F'/'f' = female, anything else other than '2' = unknown-sex, add 'male0'." argument="--update-sex">
|
|
|
6283 <option value="no_set" selected="True">Don't set</option>
|
|
|
6284 <option value="set">Set value(s)</option>
|
|
|
6285 </param>
|
|
|
6286 <when value="no_set">
|
|
|
6287 </when>
|
|
|
6288 <when value="set">
|
|
|
6289
|
|
|
6290 <param name="update_sex_MOD_0_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
6291 <param name="update_sex_MOD_1_0" type="text" label="'col-num='<n>" value="" optional="False" argument="'col-num='<n>" help=""/>
|
|
|
6292 <param name="update_sex_MOD_2_0" type="text" label="'male0'" value="" optional="False" argument="'male0'" help=""/>
|
|
|
6293 </when>
|
|
|
6294 </conditional>
|
|
|
6295 <conditional name="CONDITIONAL_real_ref_alleles">
|
|
|
6296 <param name="CONDITIONAL_SELECT_real_ref_alleles" type="select" label="Set Real ref alleles" help="Treat A2 alleles in a PLINK 1.x fileset as actual REF alleles; otherwise they're marked as provisional. " argument="--real-ref-alleles">
|
|
|
6297 <option value="no_set" selected="True">Don't set</option>
|
|
|
6298 <option value="set">Set value(s)</option>
|
|
|
6299 </param>
|
|
|
6300 <when value="no_set">
|
|
|
6301 </when>
|
|
|
6302 <when value="set">
|
|
|
6303
|
|
|
6304 </when>
|
|
|
6305 </conditional>
|
|
|
6306 <conditional name="CONDITIONAL_maj_ref">
|
|
|
6307 <param name="CONDITIONAL_SELECT_maj_ref" type="select" label="Set Maj ref" help="Set major alleles to reference, like PLINK 1.x automatically did. (Note that this is now opt-in rather than opt-out; --keep-allele-order is no longer necessary to prevent allele-swapping.) * This can only be used in runs with --make-bed/--make-[b]pgen/--export and no other commands. * By default, this only affects variants marked as having 'provisional' reference alleles. Add 'force' to apply this to all variants. * All new reference alleles are marked as provisional. " argument="--maj-ref">
|
|
|
6308 <option value="no_set" selected="True">Don't set</option>
|
|
|
6309 <option value="set">Set value(s)</option>
|
|
|
6310 </param>
|
|
|
6311 <when value="no_set">
|
|
|
6312 </when>
|
|
|
6313 <when value="set">
|
|
|
6314
|
|
|
6315 <param name="maj_ref_MOD_0_0" type="text" label="'force'" value="" optional="False" argument="'force'" help=""/>
|
|
|
6316 </when>
|
|
|
6317 </conditional>
|
|
|
6318 <conditional name="CONDITIONAL_ref_allele">
|
|
|
6319 <param name="CONDITIONAL_SELECT_ref_allele" type="select" label="Set Ref allele" help="" argument="--ref-allele">
|
|
|
6320 <option value="no_set" selected="True">Don't set</option>
|
|
|
6321 <option value="set">Set value(s)</option>
|
|
|
6322 </param>
|
|
|
6323 <when value="no_set">
|
|
|
6324 </when>
|
|
|
6325 <when value="set">
|
|
|
6326
|
|
|
6327 <param name="ref_allele_MOD_0_0" type="text" label="'force'" value="" optional="False" argument="'force'" help=""/>
|
|
|
6328 <param name="ref_allele_MOD_1_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
6329 <param name="ref_allele_MOD_2_0" type="text" label="refcol" value="" optional="False" argument="refcol" help=""/>
|
|
|
6330 <param name="ref_allele_MOD_3_0" type="text" label="IDcol" value="" optional="False" argument="IDcol" help=""/>
|
|
|
6331 <param name="ref_allele_MOD_4_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/>
|
|
|
6332 </when>
|
|
|
6333 </conditional>
|
|
|
6334 <conditional name="CONDITIONAL_alt1_allele">
|
|
|
6335 <param name="CONDITIONAL_SELECT_alt1_allele" type="select" label="Set Alt1 allele" help="These set the alleles specified in the file to ref (--ref-allele) or alt1 (--alt1-allele). They can be combined in the same run. * These can only be used in runs with --make-bed/--make-[b]pgen/--export and no other commands. * "--ref-allele <VCF filename> 4 3 '#'", which scrapes reference allele assignments from a VCF file, is especially useful. * By default, these error out when asked to change a 'known' reference allele. Add 'force' to permit that (when e.g. switching to a new reference genome). * When --alt1-allele changes the previous ref allele to alt1, the previous alt1 allele is set to reference and marked as provisional." argument="--alt1-allele">
|
|
|
6336 <option value="no_set" selected="True">Don't set</option>
|
|
|
6337 <option value="set">Set value(s)</option>
|
|
|
6338 </param>
|
|
|
6339 <when value="no_set">
|
|
|
6340 </when>
|
|
|
6341 <when value="set">
|
|
|
6342
|
|
|
6343 <param name="alt1_allele_MOD_0_0" type="text" label="'force'" value="" optional="False" argument="'force'" help=""/>
|
|
|
6344 <param name="alt1_allele_MOD_1_0" type="data" format="txt" label="filename" multiple="False" optional="True" argument="filename"/>
|
|
|
6345 <param name="alt1_allele_MOD_2_0" type="text" label="alt1col" value="" optional="False" argument="alt1col" help=""/>
|
|
|
6346 <param name="alt1_allele_MOD_3_0" type="text" label="IDcol" value="" optional="False" argument="IDcol" help=""/>
|
|
|
6347 <param name="alt1_allele_MOD_4_0" type="text" label="skip" value="" optional="False" argument="skip" help=""/>
|
|
|
6348 </when>
|
|
|
6349 </conditional>
|
|
|
6350 <conditional name="CONDITIONAL_ref_from_fa">
|
|
|
6351 <param name="CONDITIONAL_SELECT_ref_from_fa" type="select" label="Set Ref from fa" help="This sets reference alleles from the --fa file when it can be done unambiguously (note that it's never possible for deletions or some insertions). By default, it errors out when asked to change a 'known' reference allele; add the 'force' modifier to permit that. " argument="--ref-from-fa">
|
|
|
6352 <option value="no_set" selected="True">Don't set</option>
|
|
|
6353 <option value="set">Set value(s)</option>
|
|
|
6354 </param>
|
|
|
6355 <when value="no_set">
|
|
|
6356 </when>
|
|
|
6357 <when value="set">
|
|
|
6358
|
|
|
6359 <param name="ref_from_fa_MOD_0_0" type="text" label="'force'" value="" optional="False" argument="'force'" help=""/>
|
|
|
6360 </when>
|
|
|
6361 </conditional>
|
|
|
6362 <conditional name="CONDITIONAL_normalize">
|
|
|
6363 <param name="CONDITIONAL_SELECT_normalize" type="select" label="Set Normalize" help="Left-normalize all variants, using the --fa file. (alias: --norm) (Assumes no differences in capitalization.) The 'list' modifier causes a list of affected variant IDs to be written to <output prefix>.normalized." argument="--normalize">
|
|
|
6364 <option value="no_set" selected="True">Don't set</option>
|
|
|
6365 <option value="set">Set value(s)</option>
|
|
|
6366 </param>
|
|
|
6367 <when value="no_set">
|
|
|
6368 </when>
|
|
|
6369 <when value="set">
|
|
|
6370
|
|
|
6371 <param name="normalize_MOD_0_0" type="text" label="'list'" value="" optional="False" argument="'list'" help=""/>
|
|
|
6372 </when>
|
|
|
6373 </conditional>
|
|
|
6374 <conditional name="CONDITIONAL_indiv_sort">
|
|
|
6375 <param name="CONDITIONAL_SELECT_indiv_sort" type="select" label="Set Indiv sort" help="Specify sample ID sort order for merge and --make-[b]pgen/--make-bed. The following four modes are supported: * 'none'/'0' keeps samples in the order they were loaded. Default for non-merge. * 'natural'/'n' invokes "natural sort", e.g. 'id2' < 'ID3' < 'id10'. Default when merging. * 'ascii'/'a' sorts in ASCII order, e.g. 'ID3' < 'id10' < 'id2'. * 'file'/'f' uses the order in the given file (named in the last parameter). " argument="--indiv-sort">
|
|
|
6376 <option value="no_set" selected="True">Don't set</option>
|
|
|
6377 <option value="set">Set value(s)</option>
|
|
|
6378 </param>
|
|
|
6379 <when value="no_set">
|
|
|
6380 </when>
|
|
|
6381 <when value="set">
|
|
|
6382
|
|
|
6383 <param name="indiv_sort_MOD_0_0" type="text" label="mode" value="" optional="True" argument="mode" help=""/>
|
|
|
6384 <param name="indiv_sort_MOD_1_0" type="data" format="txt" label="f" multiple="False" optional="False" argument="f"/>
|
|
|
6385 </when>
|
|
|
6386 </conditional>
|
|
|
6387 <conditional name="CONDITIONAL_king_table_filter">
|
|
|
6388 <param name="CONDITIONAL_SELECT_king_table_filter" type="select" label="Set King table filter" help="Specify minimum kinship coefficient for inclusion in --make-king-table report. " argument="--king-table-filter">
|
|
|
6389 <option value="no_set" selected="True">Don't set</option>
|
|
|
6390 <option value="set">Set value(s)</option>
|
|
|
6391 </param>
|
|
|
6392 <when value="no_set">
|
|
|
6393 </when>
|
|
|
6394 <when value="set">
|
|
|
6395
|
|
|
6396 <param name="king_table_filter_MOD_0_0" type="text" label="min" value="" optional="True" argument="min" help=""/>
|
|
|
6397 </when>
|
|
|
6398 </conditional>
|
|
|
6399 <conditional name="CONDITIONAL_king_table_subset">
|
|
|
6400 <param name="CONDITIONAL_SELECT_king_table_subset" type="select" label="Set King table subset" help="Restrict current --make-king-table run to sample pairs listed in the given .kin0 file. If a second parameter is provided, only sample pairs with kinship >= that threshold (in the input .kin0) are processed. " argument="--king-table-subset">
|
|
|
6401 <option value="no_set" selected="True">Don't set</option>
|
|
|
6402 <option value="set">Set value(s)</option>
|
|
|
6403 </param>
|
|
|
6404 <when value="no_set">
|
|
|
6405 </when>
|
|
|
6406 <when value="set">
|
|
|
6407
|
|
|
6408 <param name="king_table_subset_MOD_0_0" type="data" format="txt" label="f" multiple="False" optional="True" argument="f"/>
|
|
|
6409 <param name="king_table_subset_MOD_1_0" type="text" label="kmin" value="" optional="False" argument="kmin" help=""/>
|
|
|
6410 </when>
|
|
|
6411 </conditional>
|
|
|
6412 <conditional name="CONDITIONAL_condition">
|
|
|
6413 <param name="CONDITIONAL_SELECT_condition" type="select" label="Set Condition" help="" argument="--condition">
|
|
|
6414 <option value="no_set" selected="True">Don't set</option>
|
|
|
6415 <option value="set">Set value(s)</option>
|
|
|
6416 </param>
|
|
|
6417 <when value="no_set">
|
|
|
6418 </when>
|
|
|
6419 <when value="set">
|
|
|
6420
|
|
|
6421 <param name="condition_MOD_0_0" type="text" label="variant ID" value="" optional="True" argument="variant ID" help=""/>
|
|
|
6422 <conditional name="CONDITIONAL_condition_MOD_1">
|
|
|
6423 <param name="CONDITIONAL_SELECT_condition_MOD_1" type="select" label="How to set Condition">
|
|
|
6424 <option value="no_set" selected="True">Don't set</option>
|
|
|
6425 <option value="from_list">Select from list</option>
|
|
|
6426
|
|
|
6427 </param>
|
|
|
6428 <when value="no_set">
|
|
|
6429 </when>
|
|
|
6430
|
|
|
6431 <when value="from_list">
|
|
|
6432 <param name="condition_MOD_1" type="select" label="Select value">
|
|
1
|
6433 <option value="{dominant"><![CDATA[{dominant]]></option>
|
|
|
6434 <option value="recessive}"><![CDATA[recessive}]]></option>
|
|
0
|
6435 </param>
|
|
|
6436 </when>
|
|
|
6437 </conditional>
|
|
|
6438 <param name="condition_MOD_2_0" type="text" label="'multiallelic'" value="" optional="False" argument="'multiallelic'" help=""/>
|
|
|
6439 </when>
|
|
|
6440 </conditional>
|
|
|
6441 <conditional name="CONDITIONAL_condition_list">
|
|
|
6442 <param name="CONDITIONAL_SELECT_condition_list" type="select" label="Set Condition list" help="Add the given variant, or all variants in the given file, as --glm covariates. By default, this errors out if any of the variants are multiallelic; add the 'multiallelic' ('m' for short) modifier to allow them. They'll effectively be split against the major allele (unless --glm's 'omit-ref' modifier was specified), and all induced covariate names--even for biallelic variants--will have an underscore followed by the allele code at the end." argument="--condition-list">
|
|
|
6443 <option value="no_set" selected="True">Don't set</option>
|
|
|
6444 <option value="set">Set value(s)</option>
|
|
|
6445 </param>
|
|
|
6446 <when value="no_set">
|
|
|
6447 </when>
|
|
|
6448 <when value="set">
|
|
|
6449
|
|
|
6450 <param name="condition_list_MOD_0_0" type="data" format="txt" label="fname" multiple="False" optional="True" argument="fname"/>
|
|
|
6451 <conditional name="CONDITIONAL_condition_list_MOD_1">
|
|
|
6452 <param name="CONDITIONAL_SELECT_condition_list_MOD_1" type="select" label="How to set Condition list">
|
|
|
6453 <option value="no_set" selected="True">Don't set</option>
|
|
|
6454 <option value="from_list">Select from list</option>
|
|
|
6455
|
|
|
6456 </param>
|
|
|
6457 <when value="no_set">
|
|
|
6458 </when>
|
|
|
6459
|
|
|
6460 <when value="from_list">
|
|
|
6461 <param name="condition_list_MOD_1" type="select" label="Select value">
|
|
1
|
6462 <option value="{dominant"><![CDATA[{dominant]]></option>
|
|
|
6463 <option value="recessive}"><![CDATA[recessive}]]></option>
|
|
0
|
6464 </param>
|
|
|
6465 </when>
|
|
|
6466 </conditional>
|
|
|
6467 <param name="condition_list_MOD_2_0" type="text" label="'multiallelic'" value="" optional="False" argument="'multiallelic'" help=""/>
|
|
|
6468 </when>
|
|
|
6469 </conditional>
|
|
|
6470 <conditional name="CONDITIONAL_parameters">
|
|
|
6471 <param name="CONDITIONAL_SELECT_parameters" type="select" label="Set Parameters" help="Include only the given covariates/interactions in the --glm model, identified by a list of 1-based indices and/or ranges of them. " argument="--parameters">
|
|
|
6472 <option value="no_set" selected="True">Don't set</option>
|
|
|
6473 <option value="set">Set value(s)</option>
|
|
|
6474 </param>
|
|
|
6475 <when value="no_set">
|
|
|
6476 </when>
|
|
|
6477 <when value="set">
|
|
|
6478
|
|
|
6479 <param name="parameters_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
|
|
|
6480 </when>
|
|
|
6481 </conditional>
|
|
|
6482 <conditional name="CONDITIONAL_OVERLOADED_tests">
|
|
|
6483 <param name="CONDITIONAL_OVERLOADED_SELECT_tests" type="select" label="Choose argument form for Tests" help="Overloaded argument, must chose a form">
|
|
|
6484 <option value="form_0">Form 0</option>
|
|
|
6485 <option value="form_1">Form 1</option>
|
|
|
6486 </param>
|
|
|
6487 <when value="form_0">
|
|
|
6488
|
|
|
6489 <conditional name="CONDITIONAL_tests">
|
|
|
6490 <param name="CONDITIONAL_SELECT_tests" type="select" label="Set Tests" help="Perform a (joint) test on the specified term(s) in the " argument="--tests">
|
|
|
6491 <option value="no_set" selected="True">Don't set</option>
|
|
|
6492 <option value="set">Set value(s)</option>
|
|
|
6493 </param>
|
|
|
6494 <when value="no_set">
|
|
|
6495 </when>
|
|
|
6496 <when value="set">
|
|
|
6497
|
|
|
6498 <param name="tests_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
|
|
|
6499 </when>
|
|
|
6500 </conditional>
|
|
|
6501 </when>
|
|
|
6502 <when value="form_1">
|
|
|
6503
|
|
|
6504 <conditional name="CONDITIONAL_tests">
|
|
|
6505 <param name="CONDITIONAL_SELECT_tests" type="select" label="Set Tests" help="" argument="--tests">
|
|
|
6506 <option value="no_set" selected="True">Don't set</option>
|
|
|
6507 <option value="set">Set value(s)</option>
|
|
|
6508 </param>
|
|
|
6509 <when value="no_set">
|
|
|
6510 </when>
|
|
|
6511 <when value="set">
|
|
|
6512
|
|
|
6513 </when>
|
|
|
6514 </conditional>
|
|
|
6515 </when>
|
|
|
6516 </conditional>
|
|
|
6517 <conditional name="CONDITIONAL_vif">
|
|
|
6518 <param name="CONDITIONAL_SELECT_vif" type="select" label="Set Vif" help="Set VIF threshold for --glm multicollinearity check (default 50). (This is no longer skipped for case/control phenotypes.) " argument="--vif">
|
|
|
6519 <option value="no_set" selected="True">Don't set</option>
|
|
|
6520 <option value="set">Set value(s)</option>
|
|
|
6521 </param>
|
|
|
6522 <when value="no_set">
|
|
|
6523 </when>
|
|
|
6524 <when value="set">
|
|
|
6525
|
|
|
6526 <param name="vif_MOD_0_0" type="text" label="max VIF" value="" optional="True" argument="max VIF" help=""/>
|
|
|
6527 </when>
|
|
|
6528 </conditional>
|
|
|
6529 <conditional name="CONDITIONAL_max_corr">
|
|
|
6530 <param name="CONDITIONAL_SELECT_max_corr" type="select" label="Set Max corr" help="Skip --glm regression when the absolute value of the correlation between two predictors exceeds this value (default 0.999). " argument="--max-corr">
|
|
|
6531 <option value="no_set" selected="True">Don't set</option>
|
|
|
6532 <option value="set">Set value(s)</option>
|
|
|
6533 </param>
|
|
|
6534 <when value="no_set">
|
|
|
6535 </when>
|
|
|
6536 <when value="set">
|
|
|
6537
|
|
|
6538 <param name="max_corr_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
6539 </when>
|
|
|
6540 </conditional>
|
|
|
6541 <conditional name="CONDITIONAL_xchr_model">
|
|
|
6542 <param name="CONDITIONAL_SELECT_xchr_model" type="select" label="Set Xchr model" help="Set the chrX --glm/--condition[-list]/--[v]score model. * '0' = skip chrX. * '1' = add sex as a covar on chrX, code males 0..1. * '2' (default) = chrX sex covar, code males 0..2. (Use the --glm 'interaction' modifier to test for interaction between genotype and sex.) " argument="--xchr-model">
|
|
|
6543 <option value="no_set" selected="True">Don't set</option>
|
|
|
6544 <option value="set">Set value(s)</option>
|
|
|
6545 </param>
|
|
|
6546 <when value="no_set">
|
|
|
6547 </when>
|
|
|
6548 <when value="set">
|
|
|
6549
|
|
|
6550 <param name="xchr_model_MOD_0_0" type="text" label="m" value="" optional="True" argument="m" help=""/>
|
|
|
6551 </when>
|
|
|
6552 </conditional>
|
|
|
6553 <conditional name="CONDITIONAL_adjust">
|
|
|
6554 <param name="CONDITIONAL_SELECT_adjust" type="select" label="Set Adjust" help="For each association test in this run, report some basic multiple-testing corrections, sorted in increasing-p-value order. Modifiers work the same way as they do on --adjust-file." argument="--adjust">
|
|
|
6555 <option value="no_set" selected="True">Don't set</option>
|
|
|
6556 <option value="set">Set value(s)</option>
|
|
|
6557 </param>
|
|
|
6558 <when value="no_set">
|
|
|
6559 </when>
|
|
|
6560 <when value="set">
|
|
|
6561
|
|
|
6562 <param name="adjust_MOD_0_0" type="text" label="'zs'" value="" optional="False" argument="'zs'" help=""/>
|
|
|
6563 <param name="adjust_MOD_1_0" type="text" label="'gc'" value="" optional="False" argument="'gc'" help=""/>
|
|
|
6564 <param name="adjust_MOD_2_0" type="text" label="'log10'" value="" optional="False" argument="'log10'" help=""/>
|
|
|
6565 <param name="adjust_MOD_3_0" type="text" label="'cols='<column set descriptor>" value="" optional="False" argument="'cols='<column set descriptor>" help=""/>
|
|
|
6566 </when>
|
|
|
6567 </conditional>
|
|
|
6568 <conditional name="CONDITIONAL_lambda">
|
|
|
6569 <param name="CONDITIONAL_SELECT_lambda" type="select" label="Set Lambda" help="Set genomic control lambda for --adjust[-file]. " argument="--lambda">
|
|
|
6570 <option value="no_set" selected="True">Don't set</option>
|
|
|
6571 <option value="set">Set value(s)</option>
|
|
|
6572 </param>
|
|
|
6573 <when value="no_set">
|
|
|
6574 </when>
|
|
|
6575 <when value="set">
|
|
|
6576
|
|
|
6577 </when>
|
|
|
6578 </conditional>
|
|
|
6579 <conditional name="CONDITIONAL_adjust_chr_field">
|
|
|
6580 <param name="CONDITIONAL_SELECT_adjust_chr_field" type="select" label="Set Adjust chr field" help="Set --adjust-file input field names. When " argument="--adjust-chr-field">
|
|
|
6581 <option value="no_set" selected="True">Don't set</option>
|
|
|
6582 <option value="set">Set value(s)</option>
|
|
|
6583 </param>
|
|
|
6584 <when value="no_set">
|
|
|
6585 </when>
|
|
|
6586 <when value="set">
|
|
|
6587
|
|
|
6588 <param name="adjust_chr_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
|
|
|
6589 </when>
|
|
|
6590 </conditional>
|
|
|
6591 <conditional name="CONDITIONAL_adjust_pos_field">
|
|
|
6592 <param name="CONDITIONAL_SELECT_adjust_pos_field" type="select" label="Set Adjust pos field" help="" argument="--adjust-pos-field">
|
|
|
6593 <option value="no_set" selected="True">Don't set</option>
|
|
|
6594 <option value="set">Set value(s)</option>
|
|
|
6595 </param>
|
|
|
6596 <when value="no_set">
|
|
|
6597 </when>
|
|
|
6598 <when value="set">
|
|
|
6599
|
|
|
6600 <param name="adjust_pos_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
|
|
|
6601 </when>
|
|
|
6602 </conditional>
|
|
|
6603 <conditional name="CONDITIONAL_adjust_id_field">
|
|
|
6604 <param name="CONDITIONAL_SELECT_adjust_id_field" type="select" label="Set Adjust id field" help="" argument="--adjust-id-field">
|
|
|
6605 <option value="no_set" selected="True">Don't set</option>
|
|
|
6606 <option value="set">Set value(s)</option>
|
|
|
6607 </param>
|
|
|
6608 <when value="no_set">
|
|
|
6609 </when>
|
|
|
6610 <when value="set">
|
|
|
6611
|
|
|
6612 <param name="adjust_id_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
|
|
|
6613 </when>
|
|
|
6614 </conditional>
|
|
|
6615 <conditional name="CONDITIONAL_adjust_ref_field">
|
|
|
6616 <param name="CONDITIONAL_SELECT_adjust_ref_field" type="select" label="Set Adjust ref field" help="" argument="--adjust-ref-field">
|
|
|
6617 <option value="no_set" selected="True">Don't set</option>
|
|
|
6618 <option value="set">Set value(s)</option>
|
|
|
6619 </param>
|
|
|
6620 <when value="no_set">
|
|
|
6621 </when>
|
|
|
6622 <when value="set">
|
|
|
6623
|
|
|
6624 <param name="adjust_ref_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
|
|
|
6625 </when>
|
|
|
6626 </conditional>
|
|
|
6627 <conditional name="CONDITIONAL_adjust_alt_field">
|
|
|
6628 <param name="CONDITIONAL_SELECT_adjust_alt_field" type="select" label="Set Adjust alt field" help="" argument="--adjust-alt-field">
|
|
|
6629 <option value="no_set" selected="True">Don't set</option>
|
|
|
6630 <option value="set">Set value(s)</option>
|
|
|
6631 </param>
|
|
|
6632 <when value="no_set">
|
|
|
6633 </when>
|
|
|
6634 <when value="set">
|
|
|
6635
|
|
|
6636 <param name="adjust_alt_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
|
|
|
6637 </when>
|
|
|
6638 </conditional>
|
|
|
6639 <conditional name="CONDITIONAL_adjust_a1_field">
|
|
|
6640 <param name="CONDITIONAL_SELECT_adjust_a1_field" type="select" label="Set Adjust a1 field" help="" argument="--adjust-a1-field">
|
|
|
6641 <option value="no_set" selected="True">Don't set</option>
|
|
|
6642 <option value="set">Set value(s)</option>
|
|
|
6643 </param>
|
|
|
6644 <when value="no_set">
|
|
|
6645 </when>
|
|
|
6646 <when value="set">
|
|
|
6647
|
|
|
6648 <param name="adjust_a1_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
|
|
|
6649 </when>
|
|
|
6650 </conditional>
|
|
|
6651 <conditional name="CONDITIONAL_adjust_test_field">
|
|
|
6652 <param name="CONDITIONAL_SELECT_adjust_test_field" type="select" label="Set Adjust test field" help="" argument="--adjust-test-field">
|
|
|
6653 <option value="no_set" selected="True">Don't set</option>
|
|
|
6654 <option value="set">Set value(s)</option>
|
|
|
6655 </param>
|
|
|
6656 <when value="no_set">
|
|
|
6657 </when>
|
|
|
6658 <when value="set">
|
|
|
6659
|
|
|
6660 <param name="adjust_test_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
|
|
|
6661 </when>
|
|
|
6662 </conditional>
|
|
|
6663 <conditional name="CONDITIONAL_adjust_p_field">
|
|
|
6664 <param name="CONDITIONAL_SELECT_adjust_p_field" type="select" label="Set Adjust p field" help="" argument="--adjust-p-field">
|
|
|
6665 <option value="no_set" selected="True">Don't set</option>
|
|
|
6666 <option value="set">Set value(s)</option>
|
|
|
6667 </param>
|
|
|
6668 <when value="no_set">
|
|
|
6669 </when>
|
|
|
6670 <when value="set">
|
|
|
6671
|
|
|
6672 <param name="adjust_p_field_MOD_0_0" type="text" label="n..." value="" optional="True" argument="n..." help="Multiple values are allowed"/>
|
|
|
6673 </when>
|
|
|
6674 </conditional>
|
|
|
6675 <conditional name="CONDITIONAL_ci">
|
|
|
6676 <param name="CONDITIONAL_SELECT_ci" type="select" label="Set Ci" help="Report confidence ratios for odds ratios/betas. " argument="--ci">
|
|
|
6677 <option value="no_set" selected="True">Don't set</option>
|
|
|
6678 <option value="set">Set value(s)</option>
|
|
|
6679 </param>
|
|
|
6680 <when value="no_set">
|
|
|
6681 </when>
|
|
|
6682 <when value="set">
|
|
|
6683
|
|
|
6684 <param name="ci_MOD_0_0" type="text" label="size" value="" optional="True" argument="size" help=""/>
|
|
|
6685 </when>
|
|
|
6686 </conditional>
|
|
|
6687 <conditional name="CONDITIONAL_pfilter">
|
|
|
6688 <param name="CONDITIONAL_SELECT_pfilter" type="select" label="Set Pfilter" help="Filter out assoc. test results with higher p-values. " argument="--pfilter">
|
|
|
6689 <option value="no_set" selected="True">Don't set</option>
|
|
|
6690 <option value="set">Set value(s)</option>
|
|
|
6691 </param>
|
|
|
6692 <when value="no_set">
|
|
|
6693 </when>
|
|
|
6694 <when value="set">
|
|
|
6695
|
|
|
6696 <param name="pfilter_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
6697 </when>
|
|
|
6698 </conditional>
|
|
|
6699 <conditional name="CONDITIONAL_score_col_nums">
|
|
|
6700 <param name="CONDITIONAL_SELECT_score_col_nums" type="select" label="Set Score col nums" help="Process all the specified coefficient columns in the --score file, identified by 1-based indexes and/or ranges of them. " argument="--score-col-nums">
|
|
|
6701 <option value="no_set" selected="True">Don't set</option>
|
|
|
6702 <option value="set">Set value(s)</option>
|
|
|
6703 </param>
|
|
|
6704 <when value="no_set">
|
|
|
6705 </when>
|
|
|
6706 <when value="set">
|
|
|
6707
|
|
|
6708 <param name="score_col_nums_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
|
|
|
6709 </when>
|
|
|
6710 </conditional>
|
|
|
6711 <conditional name="CONDITIONAL_q_score_range">
|
|
|
6712 <param name="CONDITIONAL_SELECT_q_score_range" type="select" label="Set Q score range" help="Apply --score to subset(s) of variants in the primary score list(s) based on e.g. p-value ranges. * The first file should have range labels in the first column, p-value lower bounds in the second column, and upper bounds in the third column. Lines with too few entries, or nonnumeric values in the second or third column, are ignored. * The second file should contain a variant ID and a p-value on each line (except possibly the first). Variant IDs are read from column #i and p-values are read from column #j, where i defaults to 1 and j defaults to i+1. The 'header' modifier causes the first nonempty line of this file to be skipped. * By default, --q-score-range errors out when a variant ID appears multiple times in the data file (and is also present in the main dataset). To use the minimum p-value in this case instead, add the 'min' modifier." argument="--q-score-range">
|
|
|
6713 <option value="no_set" selected="True">Don't set</option>
|
|
|
6714 <option value="set">Set value(s)</option>
|
|
|
6715 </param>
|
|
|
6716 <when value="no_set">
|
|
|
6717 </when>
|
|
|
6718 <when value="set">
|
|
|
6719
|
|
|
6720 <param name="q_score_range_MOD_0_0" type="text" label="range file" value="" optional="True" argument="range file" help=""/>
|
|
|
6721 <param name="q_score_range_MOD_1_0" type="text" label="data file" value="" optional="True" argument="data file" help=""/>
|
|
|
6722 <param name="q_score_range_MOD_2_0" type="text" label="i" value="" optional="False" argument="i" help=""/>
|
|
|
6723 <param name="q_score_range_MOD_3_0" type="text" label="j" value="" optional="False" argument="j" help=""/>
|
|
|
6724 <param name="q_score_range_MOD_4_0" type="text" label="'header'" value="" optional="False" argument="'header'" help=""/>
|
|
|
6725 <param name="q_score_range_MOD_5_0" type="text" label="'min'" value="" optional="False" argument="'min'" help=""/>
|
|
|
6726 </when>
|
|
|
6727 </conditional>
|
|
|
6728 <conditional name="CONDITIONAL_vscore_col_nums">
|
|
|
6729 <param name="CONDITIONAL_SELECT_vscore_col_nums" type="select" label="Set Vscore col nums" help="Process all the specified coefficient columns in the --variant-score file, identified by 1-based indexes and/or ranges of them. " argument="--vscore-col-nums">
|
|
|
6730 <option value="no_set" selected="True">Don't set</option>
|
|
|
6731 <option value="set">Set value(s)</option>
|
|
|
6732 </param>
|
|
|
6733 <when value="no_set">
|
|
|
6734 </when>
|
|
|
6735 <when value="set">
|
|
|
6736
|
|
|
6737 <param name="vscore_col_nums_MOD_0_0" type="text" label="..." value="" optional="True" argument="..." help="Multiple values are allowed"/>
|
|
|
6738 </when>
|
|
|
6739 </conditional>
|
|
|
6740 <conditional name="CONDITIONAL_memory">
|
|
|
6741 <param name="CONDITIONAL_SELECT_memory" type="select" label="Set Memory" help="Set size, in MiB, of initial workspace malloc attempt. To error out instead of reducing the request size when the initial attempt fails, add the 'require' modifier. " argument="--memory">
|
|
|
6742 <option value="no_set" selected="True">Don't set</option>
|
|
|
6743 <option value="set">Set value(s)</option>
|
|
|
6744 </param>
|
|
|
6745 <when value="no_set">
|
|
|
6746 </when>
|
|
|
6747 <when value="set">
|
|
|
6748
|
|
|
6749 <param name="memory_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
6750 <param name="memory_MOD_1_0" type="text" label="'require'" value="" optional="False" argument="'require'" help=""/>
|
|
|
6751 </when>
|
|
|
6752 </conditional>
|
|
|
6753 <conditional name="CONDITIONAL_threads">
|
|
|
6754 <param name="CONDITIONAL_SELECT_threads" type="select" label="Set Threads" help="Set maximum number of compute threads. " argument="--threads">
|
|
|
6755 <option value="no_set" selected="True">Don't set</option>
|
|
|
6756 <option value="set">Set value(s)</option>
|
|
|
6757 </param>
|
|
|
6758 <when value="no_set">
|
|
|
6759 </when>
|
|
|
6760 <when value="set">
|
|
|
6761
|
|
|
6762 <param name="threads_MOD_0_0" type="text" label="val" value="" optional="True" argument="val" help=""/>
|
|
|
6763 </when>
|
|
|
6764 </conditional>
|
|
|
6765 <conditional name="CONDITIONAL_d">
|
|
|
6766 <param name="CONDITIONAL_SELECT_d" type="select" label="Set D" help="Change variant/covariate range delimiter (normally '-'). " argument="--d">
|
|
|
6767 <option value="no_set" selected="True">Don't set</option>
|
|
|
6768 <option value="set">Set value(s)</option>
|
|
|
6769 </param>
|
|
|
6770 <when value="no_set">
|
|
|
6771 </when>
|
|
|
6772 <when value="set">
|
|
|
6773
|
|
|
6774 <param name="d_MOD_0_0" type="text" label="char" value="" optional="True" argument="char" help=""/>
|
|
|
6775 </when>
|
|
|
6776 </conditional>
|
|
|
6777 <conditional name="CONDITIONAL_seed">
|
|
|
6778 <param name="CONDITIONAL_SELECT_seed" type="select" label="Set Seed" help='Set random number seed(s). Each value must be an integer between 0 and 4294967295 inclusive. Note that --threads and "--memory require" may also be needed to reproduce some randomized runs. ' argument="--seed">
|
|
|
6779 <option value="no_set" selected="True">Don't set</option>
|
|
|
6780 <option value="set">Set value(s)</option>
|
|
|
6781 </param>
|
|
|
6782 <when value="no_set">
|
|
|
6783 </when>
|
|
|
6784 <when value="set">
|
|
|
6785
|
|
|
6786 <param name="seed_MOD_0_0" type="text" label="val..." value="" optional="True" argument="val..." help="Multiple values are allowed"/>
|
|
|
6787 </when>
|
|
|
6788 </conditional>
|
|
|
6789 <conditional name="CONDITIONAL_output_min_p">
|
|
|
6790 <param name="CONDITIONAL_SELECT_output_min_p" type="select" label="Set Output min p" help="Specify minimum p-value to write to reports. (2.23e-308 is useful for preventing underflow in some programs.) " argument="--output-min-p">
|
|
|
6791 <option value="no_set" selected="True">Don't set</option>
|
|
|
6792 <option value="set">Set value(s)</option>
|
|
|
6793 </param>
|
|
|
6794 <when value="no_set">
|
|
|
6795 </when>
|
|
|
6796 <when value="set">
|
|
|
6797
|
|
|
6798 <param name="output_min_p_MOD_0_0" type="float" label="p" value="" optional="True" argument="p" help=""/>
|
|
|
6799 </when>
|
|
|
6800 </conditional>
|
|
|
6801 <conditional name="CONDITIONAL_debug">
|
|
|
6802 <param name="CONDITIONAL_SELECT_debug" type="select" label="Set Debug" help="Use slower, more crash-resistant logging method. " argument="--debug">
|
|
|
6803 <option value="no_set" selected="True">Don't set</option>
|
|
|
6804 <option value="set">Set value(s)</option>
|
|
|
6805 </param>
|
|
|
6806 <when value="no_set">
|
|
|
6807 </when>
|
|
|
6808 <when value="set">
|
|
|
6809
|
|
|
6810 </when>
|
|
|
6811 </conditional>
|
|
|
6812 <conditional name="CONDITIONAL_randmem">
|
|
|
6813 <param name="CONDITIONAL_SELECT_randmem" type="select" label="Set Randmem" help="Randomize initial workspace memory (helps catch uninitialized-memory bugs). " argument="--randmem">
|
|
|
6814 <option value="no_set" selected="True">Don't set</option>
|
|
|
6815 <option value="set">Set value(s)</option>
|
|
|
6816 </param>
|
|
|
6817 <when value="no_set">
|
|
|
6818 </when>
|
|
|
6819 <when value="set">
|
|
|
6820
|
|
|
6821 </when>
|
|
|
6822 </conditional>
|
|
|
6823 <conditional name="CONDITIONAL_warning_errcode">
|
|
|
6824 <param name="CONDITIONAL_SELECT_warning_errcode" type="select" label="Set Warning errcode" help="Return a nonzero error code to the OS when a run completes with warning(s). " argument="--warning-errcode">
|
|
|
6825 <option value="no_set" selected="True">Don't set</option>
|
|
|
6826 <option value="set">Set value(s)</option>
|
|
|
6827 </param>
|
|
|
6828 <when value="no_set">
|
|
|
6829 </when>
|
|
|
6830 <when value="set">
|
|
|
6831
|
|
|
6832 </when>
|
|
|
6833 </conditional>
|
|
|
6834 <conditional name="CONDITIONAL_zst_level">
|
|
|
6835 <param name="CONDITIONAL_SELECT_zst_level" type="select" label="Set Zst level" help="Set the Zstd compression level (1-22, default 3). " argument="--zst-level">
|
|
|
6836 <option value="no_set" selected="True">Don't set</option>
|
|
|
6837 <option value="set">Set value(s)</option>
|
|
|
6838 </param>
|
|
|
6839 <when value="no_set">
|
|
|
6840 </when>
|
|
|
6841 <when value="set">
|
|
|
6842
|
|
|
6843 <param name="zst_level_MOD_0_0" type="text" label="lvl" value="" optional="True" argument="lvl" help=""/>
|
|
|
6844 </when>
|
|
|
6845 </conditional>
|
|
|
6846 </inputs>
|
|
|
6847 <outputs>
|
|
|
6848 <data name="OUTPUT_plink_acount __freq" format="plink.acount --freq" label="${tool.name} on ${on_string}: plink.acount --freq" from_work_dir="plink.acount --freq" hidden="True"/>
|
|
|
6849 <data name="OUTPUT_plink_adjusted __adjust_" format="plink.adjusted --adjust," label="${tool.name} on ${on_string}: plink.adjusted --adjust," from_work_dir="plink.adjusted --adjust," hidden="True"/>
|
|
|
6850 <data name="OUTPUT_plink_afreq __freq Allele" format="plink.afreq --freq Allele" label="${tool.name} on ${on_string}: plink.afreq --freq Allele" from_work_dir="plink.afreq --freq Allele" hidden="True"/>
|
|
|
6851 <data name="OUTPUT_plink_bcf __export" format="plink.bcf --export" label="${tool.name} on ${on_string}: plink.bcf --export" from_work_dir="plink.bcf --export" hidden="True"/>
|
|
|
6852 <data name="OUTPUT_plink_bed __make_bed___ PLINK" format="plink.bed --make-bed... PLINK" label="${tool.name} on ${on_string}: plink.bed --make-bed... PLINK" from_work_dir="plink.bed --make-bed... PLINK" hidden="True"/>
|
|
|
6853 <data name="OUTPUT_plink_bgen __export" format="plink.bgen --export" label="${tool.name} on ${on_string}: plink.bgen --export" from_work_dir="plink.bgen --export" hidden="True"/>
|
|
|
6854 <data name="OUTPUT_plink_bim __make_bed___ PLINK" format="plink.bim --make-bed... PLINK" label="${tool.name} on ${on_string}: plink.bim --make-bed... PLINK" from_work_dir="plink.bim --make-bed... PLINK" hidden="True"/>
|
|
|
6855 <data name="OUTPUT_plink_bin several Matrix" format="plink.bin several Matrix" label="${tool.name} on ${on_string}: plink.bin several Matrix" from_work_dir="plink.bin several Matrix" hidden="True"/>
|
|
|
6856 <data name="OUTPUT_plink_bins __freq" format="plink.bins --freq" label="${tool.name} on ${on_string}: plink.bins --freq" from_work_dir="plink.bins --freq" hidden="True"/>
|
|
|
6857 <data name="OUTPUT_plink_cov __write_covar___ Covariate" format="plink.cov --write-covar... Covariate" label="${tool.name} on ${on_string}: plink.cov --write-covar... Covariate" from_work_dir="plink.cov --write-covar... Covariate" hidden="True"/>
|
|
|
6858 <data name="OUTPUT_plink_eigenval __pca Principal" format="plink.eigenval --pca Principal" label="${tool.name} on ${on_string}: plink.eigenval --pca Principal" from_work_dir="plink.eigenval --pca Principal" hidden="True"/>
|
|
|
6859 <collection name="OUTPUT_plink_eigenvec_ __pca Principal" type="list" label="plink.eigenvec*	--pca	Principal" hidden="True">
|
|
|
6860 <discover_datasets pattern="plink\.eigenvec(?P<name>)\	\-\-pca\	Principal" format="plink.eigenvec* --pca Principal"/>
|
|
|
6861 </collection>
|
|
|
6862 <data name="OUTPUT_plink_fam __make_bed___ PLINK" format="plink.fam --make-bed... PLINK" label="${tool.name} on ${on_string}: plink.fam --make-bed... PLINK" from_work_dir="plink.fam --make-bed... PLINK" hidden="True"/>
|
|
|
6863 <data name="OUTPUT_plink_fst_summary __fst Between_population" format="plink.fst.summary --fst Between-population" label="${tool.name} on ${on_string}: plink.fst.summary --fst Between-population" from_work_dir="plink.fst.summary --fst Between-population" hidden="True"/>
|
|
|
6864 <data name="OUTPUT_plink_fst_var __fst Per_variant" format="plink.fst.var --fst Per-variant" label="${tool.name} on ${on_string}: plink.fst.var --fst Per-variant" from_work_dir="plink.fst.var --fst Per-variant" hidden="True"/>
|
|
|
6865 <data name="OUTPUT_plink_gcount __geno_counts Genotype" format="plink.gcount --geno-counts Genotype" label="${tool.name} on ${on_string}: plink.gcount --geno-counts Genotype" from_work_dir="plink.gcount --geno-counts Genotype" hidden="True"/>
|
|
|
6866 <data name="OUTPUT_plink_gen __export" format="plink.gen --export" label="${tool.name} on ${on_string}: plink.gen --export" from_work_dir="plink.gen --export" hidden="True"/>
|
|
|
6867 <data name="OUTPUT_plink_glm_firth __glm" format="plink.glm.firth --glm" label="${tool.name} on ${on_string}: plink.glm.firth --glm" from_work_dir="plink.glm.firth --glm" hidden="True"/>
|
|
|
6868 <data name="OUTPUT_plink_glm_logistic __glm" format="plink.glm.logistic --glm" label="${tool.name} on ${on_string}: plink.glm.logistic --glm" from_work_dir="plink.glm.logistic --glm" hidden="True"/>
|
|
|
6869 <data name="OUTPUT_plink_glm_logistic_hybrid __glm Logistic/Firth" format="plink.glm.logistic.hybrid --glm Logistic/Firth" label="${tool.name} on ${on_string}: plink.glm.logistic.hybrid --glm Logistic/Firth" from_work_dir="plink.glm.logistic.hybrid --glm Logistic/Firth" hidden="True"/>
|
|
|
6870 <data name="OUTPUT_plink_grm __make_grm_list GCTA" format="plink.grm --make-grm-list GCTA" label="${tool.name} on ${on_string}: plink.grm --make-grm-list GCTA" from_work_dir="plink.grm --make-grm-list GCTA" hidden="True"/>
|
|
|
6871 <data name="OUTPUT_plink_grm_N_bin __make_grm_bin GCTA" format="plink.grm.N.bin --make-grm-bin GCTA" label="${tool.name} on ${on_string}: plink.grm.N.bin --make-grm-bin GCTA" from_work_dir="plink.grm.N.bin --make-grm-bin GCTA" hidden="True"/>
|
|
|
6872 <data name="OUTPUT_plink_grm_bin __make_grm_bin GCTA" format="plink.grm.bin --make-grm-bin GCTA" label="${tool.name} on ${on_string}: plink.grm.bin --make-grm-bin GCTA" from_work_dir="plink.grm.bin --make-grm-bin GCTA" hidden="True"/>
|
|
|
6873 <collection name="OUTPUT_plink___gz few BGZipped" type="list" label="plink.*.gz	few	BGZipped" hidden="True">
|
|
|
6874 <discover_datasets pattern="plink\.(?P<name>)\.gz\	few\	BGZipped" format="plink.*.gz few BGZipped"/>
|
|
|
6875 </collection>
|
|
|
6876 <data name="OUTPUT_plink_haps __export" format="plink.haps --export" label="${tool.name} on ${on_string}: plink.haps --export" from_work_dir="plink.haps --export" hidden="True"/>
|
|
|
6877 <data name="OUTPUT_plink_hardy __hardy Hardy_Weinberg" format="plink.hardy --hardy Hardy-Weinberg" label="${tool.name} on ${on_string}: plink.hardy --hardy Hardy-Weinberg" from_work_dir="plink.hardy --hardy Hardy-Weinberg" hidden="True"/>
|
|
|
6878 <data name="OUTPUT_plink_hardy_x __hardy Graffelman_Weir" format="plink.hardy.x --hardy Graffelman-Weir" label="${tool.name} on ${on_string}: plink.hardy.x --hardy Graffelman-Weir" from_work_dir="plink.hardy.x --hardy Graffelman-Weir" hidden="True"/>
|
|
|
6879 <data name="OUTPUT_plink_het __het Inbreeding" format="plink.het --het Inbreeding" label="${tool.name} on ${on_string}: plink.het --het Inbreeding" from_work_dir="plink.het --het Inbreeding" hidden="True"/>
|
|
|
6880 <collection name="OUTPUT_plink___id lots Ordered" type="list" label="plink.*.id	lots	Ordered" hidden="True">
|
|
|
6881 <discover_datasets pattern="plink\.(?P<name>)\.id\	lots\	Ordered" format="plink.*.id lots Ordered"/>
|
|
|
6882 </collection>
|
|
|
6883 <data name="OUTPUT_plink_kin0 __make_king_table KING_robust" format="plink.kin0 --make-king-table KING-robust" label="${tool.name} on ${on_string}: plink.kin0 --make-king-table KING-robust" from_work_dir="plink.kin0 --make-king-table KING-robust" hidden="True"/>
|
|
|
6884 <data name="OUTPUT_plink_king __make_king KING_robust" format="plink.king --make-king KING-robust" label="${tool.name} on ${on_string}: plink.king --make-king KING-robust" from_work_dir="plink.king --make-king KING-robust" hidden="True"/>
|
|
|
6885 <data name="OUTPUT_plink_legend __export" format="plink.legend --export" label="${tool.name} on ${on_string}: plink.legend --export" from_work_dir="plink.legend --export" hidden="True"/>
|
|
|
6886 <data name="OUTPUT_plink_normalized __normalize" format="plink.normalized --normalize" label="${tool.name} on ${on_string}: plink.normalized --normalize" from_work_dir="plink.normalized --normalize" hidden="True"/>
|
|
|
6887 <data name="OUTPUT_plink_pgen __make_[b]pgen PLINK" format="plink.pgen --make-[b]pgen PLINK" label="${tool.name} on ${on_string}: plink.pgen --make-[b]pgen PLINK" from_work_dir="plink.pgen --make-[b]pgen PLINK" hidden="True"/>
|
|
|
6888 <data name="OUTPUT_plink_prune_in __indep_pairwise Pruned" format="plink.prune.in --indep-pairwise Pruned" label="${tool.name} on ${on_string}: plink.prune.in --indep-pairwise Pruned" from_work_dir="plink.prune.in --indep-pairwise Pruned" hidden="True"/>
|
|
|
6889 <data name="OUTPUT_plink_prune_out __indep_pairwise IDs" format="plink.prune.out --indep-pairwise IDs" label="${tool.name} on ${on_string}: plink.prune.out --indep-pairwise IDs" from_work_dir="plink.prune.out --indep-pairwise IDs" hidden="True"/>
|
|
|
6890 <data name="OUTPUT_plink_psam __make_pgen___ PLINK" format="plink.psam --make-pgen... PLINK" label="${tool.name} on ${on_string}: plink.psam --make-pgen... PLINK" from_work_dir="plink.psam --make-pgen... PLINK" hidden="True"/>
|
|
|
6891 <data name="OUTPUT_plink_pvar __make_pgen___ PLINK" format="plink.pvar --make-pgen... PLINK" label="${tool.name} on ${on_string}: plink.pvar --make-pgen... PLINK" from_work_dir="plink.pvar --make-pgen... PLINK" hidden="True"/>
|
|
|
6892 <data name="OUTPUT_plink_raw __export" format="plink.raw --export" label="${tool.name} on ${on_string}: plink.raw --export" from_work_dir="plink.raw --export" hidden="True"/>
|
|
|
6893 <data name="OUTPUT_plink_recoverid_dup __recover_var_ids List" format="plink.recoverid.dup --recover-var-ids List" label="${tool.name} on ${on_string}: plink.recoverid.dup --recover-var-ids List" from_work_dir="plink.recoverid.dup --recover-var-ids List" hidden="True"/>
|
|
|
6894 <data name="OUTPUT_plink_rel __make_rel Relationship" format="plink.rel --make-rel Relationship" label="${tool.name} on ${on_string}: plink.rel --make-rel Relationship" from_work_dir="plink.rel --make-rel Relationship" hidden="True"/>
|
|
|
6895 <data name="OUTPUT_plink_rmdup_list __rm_dup" format="plink.rmdup.list --rm-dup" label="${tool.name} on ${on_string}: plink.rmdup.list --rm-dup" from_work_dir="plink.rmdup.list --rm-dup" hidden="True"/>
|
|
|
6896 <data name="OUTPUT_plink_rmdup_mismatch __rm_dup List" format="plink.rmdup.mismatch --rm-dup List" label="${tool.name} on ${on_string}: plink.rmdup.mismatch --rm-dup List" from_work_dir="plink.rmdup.mismatch --rm-dup List" hidden="True"/>
|
|
|
6897 <data name="OUTPUT_plink_sample __export Oxford" format="plink.sample --export Oxford" label="${tool.name} on ${on_string}: plink.sample --export Oxford" from_work_dir="plink.sample --export Oxford" hidden="True"/>
|
|
|
6898 <data name="OUTPUT_plink_scount __sample_counts Sample" format="plink.scount --sample-counts Sample" label="${tool.name} on ${on_string}: plink.scount --sample-counts Sample" from_work_dir="plink.scount --sample-counts Sample" hidden="True"/>
|
|
|
6899 <data name="OUTPUT_plink_sdiff __sample_diff Sample_pair" format="plink.sdiff --sample-diff Sample-pair" label="${tool.name} on ${on_string}: plink.sdiff --sample-diff Sample-pair" from_work_dir="plink.sdiff --sample-diff Sample-pair" hidden="True"/>
|
|
|
6900 <data name="OUTPUT_plink_sdiff_summary __sample_diff Sample_pair" format="plink.sdiff.summary --sample-diff Sample-pair" label="${tool.name} on ${on_string}: plink.sdiff.summary --sample-diff Sample-pair" from_work_dir="plink.sdiff.summary --sample-diff Sample-pair" hidden="True"/>
|
|
|
6901 <data name="OUTPUT_plink_smiss __missing Sample_based" format="plink.smiss --missing Sample-based" label="${tool.name} on ${on_string}: plink.smiss --missing Sample-based" from_work_dir="plink.smiss --missing Sample-based" hidden="True"/>
|
|
|
6902 <data name="OUTPUT_plink_snplist __write_snplist List" format="plink.snplist --write-snplist List" label="${tool.name} on ${on_string}: plink.snplist --write-snplist List" from_work_dir="plink.snplist --write-snplist List" hidden="True"/>
|
|
|
6903 <data name="OUTPUT_plink_sscore __score Sample" format="plink.sscore --score Sample" label="${tool.name} on ${on_string}: plink.sscore --score Sample" from_work_dir="plink.sscore --score Sample" hidden="True"/>
|
|
|
6904 <data name="OUTPUT_plink_traw __export" format="plink.traw --export" label="${tool.name} on ${on_string}: plink.traw --export" from_work_dir="plink.traw --export" hidden="True"/>
|
|
|
6905 <data name="OUTPUT_plink_vcf __export" format="plink.vcf --export" label="${tool.name} on ${on_string}: plink.vcf --export" from_work_dir="plink.vcf --export" hidden="True"/>
|
|
|
6906 <data name="OUTPUT_plink_vmiss __missing Variant_based" format="plink.vmiss --missing Variant-based" label="${tool.name} on ${on_string}: plink.vmiss --missing Variant-based" from_work_dir="plink.vmiss --missing Variant-based" hidden="True"/>
|
|
|
6907 <data name="OUTPUT_plink_vscore __variant_score Text" format="plink.vscore --variant-score Text" label="${tool.name} on ${on_string}: plink.vscore --variant-score Text" from_work_dir="plink.vscore --variant-score Text" hidden="True"/>
|
|
|
6908 <data name="OUTPUT_plink_vscore_bin __variant_score Binary" format="plink.vscore.bin --variant-score Binary" label="${tool.name} on ${on_string}: plink.vscore.bin --variant-score Binary" from_work_dir="plink.vscore.bin --variant-score Binary" hidden="True"/>
|
|
|
6909 <data name="OUTPUT_plink_vscore_cols __variant_score Column" format="plink.vscore.cols --variant-score Column" label="${tool.name} on ${on_string}: plink.vscore.cols --variant-score Column" from_work_dir="plink.vscore.cols --variant-score Column" hidden="True"/>
|
|
|
6910 <data name="OUTPUT_plink_vscore_vars __variant_score Variant" format="plink.vscore.vars --variant-score Variant" label="${tool.name} on ${on_string}: plink.vscore.vars --variant-score Variant" from_work_dir="plink.vscore.vars --variant-score Variant" hidden="True"/>
|
|
|
6911 <collection name="OUTPUT_plink___zst pack Zstd_compressed" type="list" label="plink.*.zst	pack	Zstd-compressed" hidden="True">
|
|
|
6912 <discover_datasets pattern="plink\.(?P<name>)\.zst\	pack\	Zstd\-compressed" format="plink.*.zst pack Zstd-compressed"/>
|
|
|
6913 </collection>
|
|
|
6914 <data name="OUTPUT_plink_log" format="plink.log" label="${tool.name} on ${on_string}: plink.log" from_work_dir="plink.log" hidden="False"/>
|
|
|
6915 </outputs>
|
|
|
6916 <help><![CDATA[
|
|
|
6917 ::
|
|
|
6918
|
|
|
6919 PLINK v2.00a2.3 AVX2 (24 Jan 2020) www.cog-genomics.org/plink/2.0/
|
|
|
6920 (C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3
|
|
|
6921
|
|
|
6922 In the command line flag definitions that follow,
|
|
|
6923 * <angle brackets> denote a required parameter, where the text between the
|
|
|
6924 angle brackets describes its nature.
|
|
|
6925 * ['square brackets + single-quotes'] denotes an optional modifier. Use the
|
|
|
6926 EXACT text in the quotes.
|
|
|
6927 * [{bar|separated|braced|bracketed|values}] denotes a collection of mutually
|
|
|
6928 exclusive optional modifiers (again, the exact text must be used). When
|
|
|
6929 there are no outer square brackets, one of the choices must be selected.
|
|
|
6930 * ['quoted_text='<description of value>] denotes an optional modifier that
|
|
|
6931 must begin with the quoted text, and be followed by a value with no
|
|
|
6932 whitespace in between. '|' may also be used here to indicate mutually
|
|
|
6933 exclusive options.
|
|
|
6934 * [square brackets without quotes or braces] denote an optional parameter,
|
|
|
6935 where the text between the brackets describes its nature.
|
|
|
6936 * An ellipsis (...) indicates that you may enter multiple parameters of the
|
|
|
6937 specified type.
|
|
|
6938 * A "column set descriptor" is either
|
|
|
6939 1. a comma-separated sequence of column set names; this is interpreted as
|
|
|
6940 the full list of column sets to include.
|
|
|
6941 2. a comma-separated sequence of column set names, all preceded by '+' or
|
|
|
6942 '-'; this is interpreted as a list of changes to the default.
|
|
|
6943
|
|
|
6944 plink2 <input flag(s)...> [command flag(s)...] [other flag(s)...]
|
|
|
6945 plink2 --help [flag name(s)...]
|
|
|
6946
|
|
|
6947 Most PLINK runs require exactly one main input fileset. The following flags
|
|
|
6948 are available for defining its form and location:
|
|
|
6949
|
|
|
6950 --pfile <prefix> ['vzs'] : Specify .pgen + .pvar[.zst] + .psam prefix.
|
|
|
6951 --pgen <filename> : Specify full name of .pgen/.bed file.
|
|
|
6952 --pvar <filename> : Specify full name of .pvar/.bim file.
|
|
|
6953 --psam <filename> : Specify full name of .psam/.fam file.
|
|
|
6954
|
|
|
6955 --bfile <prefix> ['vzs'] : Specify .bed + .bim[.zst] + .fam prefix.
|
|
|
6956 --bpfile <prefix> ['vzs'] : Specify .pgen + .bim[.zst] + .fam prefix.
|
|
|
6957
|
|
|
6958 --keep-autoconv : When importing non-PLINK-binary data, don't delete
|
|
|
6959 autogenerated binary fileset at end of run.
|
|
|
6960
|
|
|
6961 --no-fid : .fam file does not contain column 1 (family ID).
|
|
|
6962 --no-parents : .fam file does not contain columns 3-4 (parents).
|
|
|
6963 --no-sex : .fam file does not contain column 5 (sex).
|
|
|
6964
|
|
|
6965 --vcf <filename> ['dosage='<field>]
|
|
|
6966 --bcf <filename> ['dosage='<field>] (not implemented yet) :
|
|
|
6967 Specify full name of .vcf{|.gz|.zst} or BCF2 file to import.
|
|
|
6968 * These can be used with --psam/--fam.
|
|
|
6969 * By default, dosage information is not imported. To import the GP field
|
|
|
6970 (must be VCFv4.3-style 0..1, one probability per possible genotype), add
|
|
|
6971 'dosage=GP' (or 'dosage=GP-force', see below). To import Minimac3-style
|
|
|
6972 DS+HDS phased dosage, add 'dosage=HDS'. 'dosage=DS' (or anything else
|
|
|
6973 for now) causes the named field to be interpreted as a Minimac3-style
|
|
|
6974 dosage.
|
|
|
6975 Note that, in the dosage=GP case, PLINK 2 collapses the probabilities
|
|
|
6976 down to dosages; you cannot use PLINK 2 to losslessly convert VCF
|
|
|
6977 FORMAT:GP data to e.g. BGEN format. To make this more obvious, PLINK 2
|
|
|
6978 now errors out when dosage=GP is used on a file with a FORMAT:DS header
|
|
|
6979 line and --import-dosage-certainty wasn't specified, since dosage=DS
|
|
|
6980 extracts the same information more quickly in this situation. You can
|
|
|
6981 suppress this error with 'dosage=GP-force'.
|
|
|
6982 In all of these cases, hardcalls are regenerated from scratch from the
|
|
|
6983 dosages. As a consequence, variants with no GT field can now be
|
|
|
6984 imported; they will be assumed to contain only diploid calls when HDS is
|
|
|
6985 also absent.
|
|
|
6986
|
|
|
6987 --data <filename prefix> [REF/ALT mode] ['gzs']
|
|
|
6988 --bgen <filename> [REF/ALT mode] ['snpid-chr']
|
|
|
6989 --gen <filename> [REF/ALT mode]
|
|
|
6990 --sample <filename> :
|
|
|
6991 Specify an Oxford-format dataset to import. --data specifies a .gen[.zst]
|
|
|
6992 + .sample pair, while --bgen specifies a BGEN v1.1+ file.
|
|
|
6993 * If a BGEN v1.2+ file contains sample IDs, it may be imported without a
|
|
|
6994 companion .sample file.
|
|
|
6995 * With 'snpid-chr', chromosome codes are read from the 'SNP ID' field
|
|
|
6996 instead of the usual chromosome field.
|
|
|
6997 * The following REF/ALT modes are supported:
|
|
|
6998 'ref-first': The first allele for each variant is REF.
|
|
|
6999 'ref-last': The last allele for each variant is REF.
|
|
|
7000 'ref-unknown' (default): The last allele for each variant is treated as
|
|
|
7001 provisional-REF.
|
|
|
7002 This parameter will be required instead of optional in alpha 3.
|
|
|
7003
|
|
|
7004 --haps <filename> [{ref-first | ref-last}]
|
|
|
7005 --legend <filename> <chr code> :
|
|
|
7006 Specify .haps [+ .legend] file(s) to import.
|
|
|
7007 * When --legend is specified, it's assumed that the --haps file doesn't
|
|
|
7008 contain header columns.
|
|
|
7009 * On chrX, the second male column may contain dummy '-' entries. (However,
|
|
|
7010 PLINK 2 currently cannot handle omitted male columns.)
|
|
|
7011 * If not used with --sample, new sample IDs are of the form 'per#/per#'.
|
|
|
7012
|
|
|
7013 --map <filename> : Specify full name of .map file.
|
|
|
7014 --import-dosage <allele dosage file> ['noheader'] ['id-delim='<char>]
|
|
|
7015 ['skip0='<i>] ['skip1='<j>] ['skip2='<k>] ['dose1']
|
|
|
7016 ['format='<m>] [{ref-first | ref-last}]
|
|
|
7017 ['single-chr='<code>] ['chr-col-num='<#>]
|
|
|
7018 ['pos-col-num='<#>] :
|
|
|
7019 Specify PLINK 1.x-style dosage file to import.
|
|
|
7020 * You must also specify a companion .psam/.fam file.
|
|
|
7021 * By default, PLINK assumes that the file contains a header line, which has
|
|
|
7022 'SNP' in (1-based) column i+1, 'A1' in column i+j+2, 'A2' in column
|
|
|
7023 i+j+3, and sample FID/IIDs starting from column i+j+k+4. (i/j/k are
|
|
|
7024 normally zero, but can be changed with 'skip0', 'skip1', and 'skip2'
|
|
|
7025 respectively. FID/IID are normally assumed to be separate tokens, but if
|
|
|
7026 they're merged into a single token you can specify the delimiter with
|
|
|
7027 'id-delim='.) If such a header line is not present, use the 'noheader'
|
|
|
7028 modifier; samples will then be assumed to appear in the same order as
|
|
|
7029 they do in the .psam/.fam file.
|
|
|
7030 * You may specify a companion .map file. If you do not,
|
|
|
7031 * 'single-chr=' can be used to specify that all variants are on the named
|
|
|
7032 chromosome. Otherwise, you can use 'chr-col-num=' to read chromosome
|
|
|
7033 codes from the given (1-based) column number.
|
|
|
7034 * 'pos-col-num=' causes bp coordinates to be read from the given column
|
|
|
7035 number.
|
|
|
7036 * The 'format=' modifier lets you specify the number of values used to
|
|
|
7037 represent each dosage. 'format=1' normally indicates a single 0..2 A1
|
|
|
7038 expected count; 'dose1' modifies this to a 0..1 frequency. 'format=2'
|
|
|
7039 indicates a 0..1 homozygous A1 likelihood followed by a 0..1 het
|
|
|
7040 likelihood. 'format=3' indicates 0..1 hom A1, 0..1 het, 0..1 hom A2.
|
|
|
7041 'format=infer' (the default) infers the format from the number of columns
|
|
|
7042 in the first nonheader line.
|
|
|
7043
|
|
|
7044 --dummy <sample ct> <SNP ct> [missing dosage freq] [missing pheno freq]
|
|
|
7045 [{acgt | 1234 | 12}] ['pheno-ct='<count>] ['scalar-pheno']
|
|
|
7046 ['dosage-freq='<rate>]
|
|
|
7047 This generates a fake input dataset with the specified number of samples
|
|
|
7048 and SNPs.
|
|
|
7049 * By default, the missing dosage and phenotype frequencies are zero.
|
|
|
7050 These can be changed by providing 3rd and 4th numeric parameters.
|
|
|
7051 * By default, allele codes are As and Bs; this can be changed with the
|
|
|
7052 'acgt', '1234', or '12' modifier.
|
|
|
7053 * By default, one binary phenotype is generated. 'pheno-ct=' can be used
|
|
|
7054 to change the number of phenotypes, and 'scalar-pheno' causes these
|
|
|
7055 phenotypes to be normally distributed scalars.
|
|
|
7056 * By default, all (nonmissing) dosages are in {0,1,2}. To make some of
|
|
|
7057 them take on decimal values, use 'dosage-freq='. (These dosages are
|
|
|
7058 affected by --hard-call-threshold and --dosage-erase-threshold.)
|
|
|
7059
|
|
|
7060 --fa <filename> : Specify full name of reference FASTA file.
|
|
|
7061
|
|
|
7062 Output files have names of the form 'plink2.<extension>' by default. You can
|
|
|
7063 change the 'plink2' prefix with
|
|
|
7064
|
|
|
7065 --out <prefix> : Specify prefix for output files.
|
|
|
7066
|
|
|
7067 Most runs also require at least one of the following commands:
|
|
|
7068
|
|
|
7069 --rm-dup [mode] ['list']
|
|
|
7070 Remove all but one instance of each duplicate-ID variant (ignoring the
|
|
|
7071 missing ID), and (with the 'list' modifier) write a list of duplicated IDs
|
|
|
7072 to <output prefix>.rmdup.list.
|
|
|
7073 The following modes of operation are supported:
|
|
|
7074 * 'error' (default) causes this to error out when there's a genotype data
|
|
|
7075 or other mismatch between the records. A list of affected IDs is written
|
|
|
7076 to <output prefix>.rmdup.mismatch.
|
|
|
7077 * 'retain-mismatch' causes all instances of a duplicate-ID variant to be
|
|
|
7078 retained when there's a genotype data or variant info mismatch; otherwise
|
|
|
7079 one instance is kept. The .rmdup.mismatch file is also written.
|
|
|
7080 * 'exclude-mismatch' removes all instances of duplicate-ID mismatched
|
|
|
7081 variants instead.
|
|
|
7082 * 'exclude-all' causes all instances of duplicate-ID variants to be
|
|
|
7083 removed, even when the actual records are identical.
|
|
|
7084 * 'force-first' causes only the first instance of duplicate-ID variants to
|
|
|
7085 be kept, under all circumstances.
|
|
|
7086
|
|
|
7087 --make-pgen ['vzs'] ['format='<code>] ['trim-alts'] ['erase-phase']
|
|
|
7088 ['erase-dosage'] ['pvar-cols='<col set descriptor>]
|
|
|
7089 ['psam-cols='<col set descriptor>]
|
|
|
7090 --make-bpgen ['vzs'] ['format='<code>] ['trim-alts'] ['erase-phase']
|
|
|
7091 ['erase-dosage']
|
|
|
7092 --make-bed ['vzs'] ['trim-alts']
|
|
|
7093 Create a new PLINK binary fileset (--make-pgen = .pgen + .pvar[.zst] +
|
|
|
7094 .psam, --make-bpgen = .pgen + .bim[.zst] + .fam).
|
|
|
7095 * Unlike the automatic text-to-binary converters (which only heed
|
|
|
7096 chromosome filters), this supports all of PLINK's filtering flags.
|
|
|
7097 * The 'vzs' modifier causes the variant file (.pvar/.bim) to be
|
|
|
7098 Zstd-compressed.
|
|
|
7099 * The 'format' modifier requests an uncompressed fixed-variant-width .pgen
|
|
|
7100 file. (These do not directly support multiallelic variants.) The
|
|
|
7101 following format code is currently supported:
|
|
|
7102 2: just like .bed, except with an extended (12-byte instead of 3-byte)
|
|
|
7103 header containing variant/sample counts, and rotated genotype codes
|
|
|
7104 (00 = hom ref, 01 = het, 10 = hom alt, 11 = missing).
|
|
|
7105 * The 'erase-phase' and 'erase-dosage' modifiers prevent phase and dosage
|
|
|
7106 information from being written to the new .pgen.
|
|
|
7107 * The first five columns of a .pvar file are always #CHROM/POS/ID/REF/ALT.
|
|
|
7108 Supported optional .pvar column sets are:
|
|
|
7109 xheader: All ## header lines (yeah, this is technically not a column),
|
|
|
7110 except for possibly FILTER/INFO definitions when those
|
|
|
7111 column(s) have been removed. Without this, only the #CHROM
|
|
|
7112 header line is kept.
|
|
|
7113 maybequal: QUAL. Omitted if all remaining values are missing.
|
|
|
7114 qual: Force QUAL column to be written even when empty.
|
|
|
7115 maybefilter: FILTER. Omitted if all remaining values are missing.
|
|
|
7116 filter: Force FILTER column to be written even when empty.
|
|
|
7117 maybeinfo: INFO. Omitted if all remaining values are missing, or if
|
|
|
7118 INFO:PR is the only subfield.
|
|
|
7119 info: Force INFO column to be written.
|
|
|
7120 maybecm: Centimorgan coordinate. Omitted if all remaining values = 0.
|
|
|
7121 cm: Force CM column to be written even when empty.
|
|
|
7122 The default is xheader,maybequal,maybefilter,maybeinfo,maybecm.
|
|
|
7123 * Supported column sets for the .psam file are:
|
|
|
7124 maybefid: Family ID, '0' = missing. Omitted if all values missing.
|
|
|
7125 fid: Force FID column to be written even when empty.
|
|
|
7126 maybesid: Source ID, '0' = missing. Omitted if all values missing.
|
|
|
7127 sid: Force SID column to be written even when empty.
|
|
|
7128 maybeparents: Father and mother IIDs. Omitted if all values missing.
|
|
|
7129 parents: Force PAT and MAT columns to be written even when empty.
|
|
|
7130 sex: '1' = male, '2' = female, 'NA' = missing.
|
|
|
7131 pheno1: First active phenotype. If none, all column entries are set to
|
|
|
7132 the --output-missing-phenotype string.
|
|
|
7133 phenos: All active phenotypes, if any. (Can be combined with pheno1 to
|
|
|
7134 force at least one phenotype column to be written.)
|
|
|
7135 The default is maybefid,maybesid,maybeparents,sex,phenos.
|
|
|
7136
|
|
|
7137 --make-just-pvar ['zs'] ['cols='<column set descriptor>]
|
|
|
7138 --make-just-psam ['cols='<column set descriptor>]
|
|
|
7139 --make-just-bim ['zs']
|
|
|
7140 --make-just-fam
|
|
|
7141 Variants of --make-pgen/--make-bed which only write a new variant or sample
|
|
|
7142 file. These don't always require an input genotype file.
|
|
|
7143 USE THESE CAUTIOUSLY. It is very easy to desynchronize your binary
|
|
|
7144 genotype data and your sample/variant indexes if you use these commands
|
|
|
7145 improperly. If you have any doubt, stick with --make-[b]pgen/--make-bed.
|
|
|
7146
|
|
|
7147 --export <output format(s)...> [{01 | 12}] ['bgz'] ['id-delim='<char>]
|
|
|
7148 ['id-paste='<column set descriptor>] ['include-alt']
|
|
|
7149 ['omit-nonmale-y'] ['spaces'] ['vcf-dosage='<field>] ['ref-first']
|
|
|
7150 ['bits='<#>]
|
|
|
7151 Create a new fileset with all filters applied. The following output
|
|
|
7152 formats are supported:
|
|
|
7153 (actually, only A, AD, A-transpose, bgen-1.x, ind-major-bed, haps,
|
|
|
7154 hapslegend, oxford, and vcf are implemented for now)
|
|
|
7155 * '23': 23andMe 4-column format. This can only be used on a single
|
|
|
7156 sample's data (--keep may be handy), and does not support
|
|
|
7157 multicharacter allele codes.
|
|
|
7158 * 'A': Sample-major additive (0/1/2) coding, suitable for loading from R.
|
|
|
7159 If you need uncounted alleles to be named in the header line, add
|
|
|
7160 the 'include-alt' modifier.
|
|
|
7161 * 'AD': Sample-major additive (0/1/2) + dominant (het=1/hom=0) coding.
|
|
|
7162 Also supports 'include-alt'.
|
|
|
7163 * 'A-transpose': Variant-major 0/1/2.
|
|
|
7164 * 'beagle': Unphased per-autosome .dat and .map files, readable by early
|
|
|
7165 BEAGLE versions.
|
|
|
7166 * 'beagle-nomap': Single .beagle.dat file.
|
|
|
7167 * 'bgen-1.x': Oxford-format .bgen + .sample. For v1.2/v1.3, sample
|
|
|
7168 identifiers are stored in the .bgen (with id-delim and
|
|
|
7169 id-paste settings applied), and default precision is 16-bit
|
|
|
7170 (use the 'bits' modifier to reduce this).
|
|
|
7171 * 'bimbam': Regular BIMBAM format.
|
|
|
7172 * 'bimbam-1chr': BIMBAM format, with a two-column .pos.txt file. Does not
|
|
|
7173 support multiple chromosomes.
|
|
|
7174 * 'fastphase': Per-chromosome fastPHASE files, with
|
|
|
7175 .chr-<chr #>.phase.inp filename extensions.
|
|
|
7176 * 'fastphase-1chr': Single .phase.inp file. Does not support
|
|
|
7177 multiple chromosomes.
|
|
|
7178 * 'haps', 'hapslegend': Oxford-format .haps + .sample[ + .legend]. All
|
|
|
7179 data must be biallelic and phased. When the 'bgz'
|
|
|
7180 modifier is present, the .haps file is
|
|
|
7181 block-gzipped.
|
|
|
7182 * 'HV': Per-chromosome Haploview files, with .chr-<chr #>{.ped,.info}
|
|
|
7183 filename extensions.
|
|
|
7184 * 'HV-1chr': Single Haploview .ped + .info file pair. Does not support
|
|
|
7185 multiple chromosomes.
|
|
|
7186 * 'ind-major-bed': PLINK 1 sample-major .bed (+ .bim + .fam).
|
|
|
7187 * 'lgen': PLINK 1 long-format (.lgen + .fam + .map), loadable with --lfile.
|
|
|
7188 * 'lgen-ref': .lgen + .fam + .map + .ref, loadable with --lfile +
|
|
|
7189 --reference.
|
|
|
7190 * 'list': Single genotype-based list, up to 4 lines per variant. To omit
|
|
|
7191 nonmale genotypes on the Y chromosome, add the 'omit-nonmale-y'
|
|
|
7192 modifier.
|
|
|
7193 * 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a
|
|
|
7194 genotype-based list which omits the most common genotype for
|
|
|
7195 each variant. Also supports 'omit-nonmale-y'.
|
|
|
7196 * 'oxford': Oxford-format .gen + .sample. When the 'bgz' modifier is
|
|
|
7197 present, the .gen file is block-gzipped.
|
|
|
7198 * 'ped': PLINK 1 sample-major (.ped + .map), loadable with --file.
|
|
|
7199 * 'compound-genotypes': Same as 'ped', except that the space between each
|
|
|
7200 pair of same-variant allele codes is removed.
|
|
|
7201 * 'structure': Structure-format.
|
|
|
7202 * 'transpose': PLINK 1 variant-major (.tped + .tfam), loadable with
|
|
|
7203 --tfile.
|
|
|
7204 * 'vcf', 'vcf-4.2': VCF (default version 4.3). If PAR1 and PAR2 are
|
|
|
7205 present, they are automatically merged with chrX, with
|
|
|
7206 proper handling of chromosome codes and male ploidy.
|
|
|
7207 When the 'bgz' modifier is present, the VCF file is
|
|
|
7208 block-gzipped.
|
|
|
7209 The 'id-paste' modifier controls which .psam columns
|
|
|
7210 are used to construct sample IDs (choices are maybefid,
|
|
|
7211 fid, iid, maybesid, and sid; default is
|
|
|
7212 maybefid,iid,maybesid), while the 'id-delim' modifier
|
|
|
7213 sets the character between the ID pieces (default '_').
|
|
|
7214 Dosages are not exported unless the 'vcf-dosage='
|
|
|
7215 modifier is present. The following five dosage export
|
|
|
7216 modes are supported:
|
|
|
7217 'GP': genotype posterior probabilities (v4.3 only).
|
|
|
7218 'DS': Minimac3-style dosages, omitted for hardcalls.
|
|
|
7219 'DS-force': Minimac3-style dosages, never omit.
|
|
|
7220 'HDS': Minimac3-style phased dosages, omitted for
|
|
|
7221 hardcalls and unphased calls. Also includes
|
|
|
7222 'DS' output.
|
|
|
7223 'HDS-force': Always report DS and HDS.
|
|
|
7224 In addition,
|
|
|
7225 * The '12' modifier causes alt1 alleles to be coded as '1' and ref alleles
|
|
|
7226 to be coded as '2', while '01' maps alt1 -> 0 and ref -> 1.
|
|
|
7227 * The 'spaces' modifier makes the output space-delimited instead of
|
|
|
7228 tab-delimited, whenever both are permitted.
|
|
|
7229 * For biallelic formats where it's unspecified whether the reference/major
|
|
|
7230 allele should appear first or second, --export defaults to second for
|
|
|
7231 compatibility with PLINK 1.9. Use 'ref-first' to change this.
|
|
|
7232 (Note that this doesn't apply to the 'A', 'AD', and 'A-transpose'
|
|
|
7233 formats; use --export-allele to control which alleles are counted there.)
|
|
|
7234
|
|
|
7235 --freq ['zs'] ['counts'] ['cols='<column set descriptor>] ['bins-only']
|
|
|
7236 ['refbins='<comma-separated bin boundaries> | 'refbins-file='<file>]
|
|
|
7237 ['alt1bins='<comma-separated bin boundaries> | 'alt1bins-file='<file>]
|
|
|
7238 Empirical allele frequency report. By default, only founders are
|
|
|
7239 considered. Dosages are taken into account (e.g. heterozygous haploid
|
|
|
7240 calls count as 0.5).
|
|
|
7241 Supported column sets are:
|
|
|
7242 chrom: Chromosome ID.
|
|
|
7243 pos: Base-pair coordinate.
|
|
|
7244 (ID is always present, and positioned here.)
|
|
|
7245 ref: Reference allele.
|
|
|
7246 alt1: Alternate allele 1.
|
|
|
7247 alt: All alternate alleles, comma-separated.
|
|
|
7248 reffreq: Reference allele frequency/dosage.
|
|
|
7249 alt1freq: Alt1 frequency/dosage.
|
|
|
7250 altfreq: Comma-separated frequencies/dosages for all alternate alleles.
|
|
|
7251 freq: Similar to altfreq, except ref is also included at the start.
|
|
|
7252 eq: Comma-separated <allele>=<freq> for all present alleles. (If no
|
|
|
7253 alleles are present, the column contains a single '.'.)
|
|
|
7254 eqz: Same as eq, except zero-counts are included.
|
|
|
7255 alteq/alteqz: Same as eq/eqz, except reference allele is omitted.
|
|
|
7256 numeq: 0=<freq>,1=<freq>, etc. Zero-counts are omitted.
|
|
|
7257 altnumeq: Same as numeq, except reference allele is omitted.
|
|
|
7258 machr2: Unphased MaCH imputation quality metric.
|
|
|
7259 minimac3r2: Phased Minimac3 imputation quality.
|
|
|
7260 nobs: Number of allele observations.
|
|
|
7261 The default is chrom,ref,alt,altfreq,nobs.
|
|
|
7262 Additional .afreq.{ref,alt1}.bins (or .acount.{ref,alt1}.bins with
|
|
|
7263 'counts') file(s) are generated when 'refbins='/'refbins-file=' or
|
|
|
7264 'alt1bins='/'alt1bins-file=' is present; these report the total number of
|
|
|
7265 frequencies or counts in each left-closed, right-open interval. (If you
|
|
|
7266 only want these histogram(s), and not the main report, add 'bins-only'.)
|
|
|
7267
|
|
|
7268 --geno-counts ['zs'] ['cols='<column set descriptor>]
|
|
|
7269 Variant-based hardcall genotype count report (considering both alleles
|
|
|
7270 simultaneously in the diploid case). Nonfounders are now included; use
|
|
|
7271 --keep-founders if this is a problem. Heterozygous haploid calls are
|
|
|
7272 treated as missing.
|
|
|
7273 Supported column sets are:
|
|
|
7274 chrom: Chromosome ID.
|
|
|
7275 pos: Base-pair coordinate.
|
|
|
7276 (ID is always present, and positioned here.)
|
|
|
7277 ref: Reference allele.
|
|
|
7278 alt1: Alternate allele 1.
|
|
|
7279 alt: All alternate alleles, comma-separated.
|
|
|
7280 homref: Homozygous-ref count.
|
|
|
7281 refalt1: Heterozygous ref-alt1 count.
|
|
|
7282 refalt: Comma-separated het ref-altx counts.
|
|
|
7283 homalt1: Homozygous-alt1 count.
|
|
|
7284 altxy: Comma-separated altx-alty counts, in (1/1)-(1/2)-(2/2)-(1/3)-...
|
|
|
7285 order.
|
|
|
7286 xy: Similar to altxy, except the reference allele is treated as alt0,
|
|
|
7287 and the sequence starts (0/0)-(0/1)-(1/1)-(0/2)-...
|
|
|
7288 hapref: Haploid-ref count.
|
|
|
7289 hapalt1: Haploid-alt1 count.
|
|
|
7290 hapalt: Comma-separated haploid-altx counts.
|
|
|
7291 hap: Similar to hapalts, except ref is also included at the start.
|
|
|
7292 numeq: 0/0=<hom ref ct>,0/1=<het ref-alt1>,1/1=<hom alt1>,...,0=<hap ref>
|
|
|
7293 etc. Zero-counts are omitted. (If all genotypes are missing, the
|
|
|
7294 column contains a single '.'.)
|
|
|
7295 missing: Number of missing genotypes.
|
|
|
7296 nobs: Number of (nonmissing) genotype observations.
|
|
|
7297 The default is chrom,ref,alt,homref,refalt,altxy,hapref,hapalt,missing.
|
|
|
7298
|
|
|
7299 --sample-counts ['zs'] ['cols='<column set descriptor>]
|
|
|
7300 Sample-based hardcall genotype count report.
|
|
|
7301 * Unknown-sex samples are treated as female.
|
|
|
7302 * Heterozygous haploid calls (MT included) are treated as missing.
|
|
|
7303 * As with other PLINK 2 commands, SNPs that have not been left-normalized
|
|
|
7304 are counted as non-SNP non-symbolic. (Use e.g. --normalize when that's a
|
|
|
7305 problem.)
|
|
|
7306 * Supported column sets are:
|
|
|
7307 maybefid: FID, if that column was present in the input.
|
|
|
7308 fid: Force FID column to be written even when absent in the input.
|
|
|
7309 (IID is always present, and positioned here.)
|
|
|
7310 maybesid: SID, if that column was present in the input.
|
|
|
7311 sid: Force SID column to be written even when absent in the input.
|
|
|
7312 sex: '1' = male, '2' = female, 'NA' = missing.
|
|
|
7313 hom: Homozygous genotype count.
|
|
|
7314 homref: Homozygous-ref genotype count.
|
|
|
7315 homalt: Homozygous-alt genotype count.
|
|
|
7316 homaltsnp: Homozygous-alt SNP count.
|
|
|
7317 het: Heterozygous genotype count.
|
|
|
7318 refalt: Heterozygous ref-altx genotype count.
|
|
|
7319 het2alt: Heterozygous altx-alty genotype count.
|
|
|
7320 hetsnp: Heterozygous SNP count.
|
|
|
7321 dipts: Diploid SNP transition count.
|
|
|
7322 ts: SNP transition count (excluding chrY for females).
|
|
|
7323 diptv: Diploid SNP transversion count.
|
|
|
7324 tv: SNP transversion count.
|
|
|
7325 dipnonsnpsymb: Diploid non-SNP, non-symbolic count.
|
|
|
7326 nonsnpsymb: Non-SNP, non-symbolic count.
|
|
|
7327 symbolic: Symbolic variant count.
|
|
|
7328 nonsnp: Non-SNP count.
|
|
|
7329 dipsingle: Number of singletons relative to this dataset, across just
|
|
|
7330 diploid calls. (Note that if the ALT allele in a chrX
|
|
|
7331 biallelic variant appears in exactly one female and one
|
|
|
7332 male, that counts as a singleton for just the female.)
|
|
|
7333 single: Number of singletons relative to this dataset.
|
|
|
7334 haprefwfemaley: Haploid-ref count, counting chrY for everyone.
|
|
|
7335 hapref: Haploid-ref count, excluding chrY for females.
|
|
|
7336 hapaltwfemaley: Haploid-alt count, counting chrY for everyone.
|
|
|
7337 hapalt: Haploid-alt count, excluding chrY for females.
|
|
|
7338 missingwfemaley: Missing call count, counting chrY for everyone.
|
|
|
7339 missing: Missing call count, excluding chrY for females.
|
|
|
7340 The default is maybefid,maybesid,homref,homaltsnp,hetsnp,dipts,diptv,
|
|
|
7341 dipnonsnpsymb,dipsingle,haprefwfemaley,hapaltwfemaley,missingwfemaley.
|
|
|
7342 * The 'hetsnp', 'dipts'/'ts'/'diptv'/'tv', 'dipnonsnpsymb'/'nonsnpsymb',
|
|
|
7343 'symbolic', and 'nonsnp' columns count each ALT allele in a heterozygous
|
|
|
7344 altx-alty call separately, since they can be of different subtypes.
|
|
|
7345 (I.e. if they are of the same subtype, the corresponding count is
|
|
|
7346 incremented by 2.) As a consequence, these columns are unaffected by
|
|
|
7347 variant split/join.
|
|
|
7348
|
|
|
7349 --missing ['zs'] [{sample-only | variant-only}]
|
|
|
7350 ['scols='<column set descriptor>] ['vcols='<column set descriptor>]
|
|
|
7351 Generate sample- and variant-based missing data reports (or just one report
|
|
|
7352 if 'sample-only'/'variant-only' is specified).
|
|
|
7353 As of alpha 2, mixed MT hardcalls appear in the heterozygous haploid stats.
|
|
|
7354 Supported column sets in the sample-based report are:
|
|
|
7355 maybefid: FID, if that column was present in the input.
|
|
|
7356 fid: Force FID column to be written even when absent in the input.
|
|
|
7357 (IID is always present, and positioned here.)
|
|
|
7358 maybesid: SID, if that column was present in the input.
|
|
|
7359 sid: Force SID column to be written even when absent in the input.
|
|
|
7360 misspheno1: First active phenotype missing (Y/N)? Always 'Y' if no
|
|
|
7361 phenotypes are loaded.
|
|
|
7362 missphenos: A Y/N column for each loaded phenotype. (Can be combined
|
|
|
7363 with misspheno1 to force at least one such column.)
|
|
|
7364 nmissdosage: Number of missing dosages.
|
|
|
7365 nmiss: Number of missing hardcalls, not counting het haploids.
|
|
|
7366 nmisshh: Number of missing hardcalls, counting het haploids.
|
|
|
7367 hethap: Number of heterozygous haploid hardcalls.
|
|
|
7368 nobs: Denominator (male count on chrY, otherwise total sample count).
|
|
|
7369 fmissdosage: Missing dosage rate.
|
|
|
7370 fmiss: Missing hardcall rate, not counting het haploids.
|
|
|
7371 fmisshh: Missing hardcall rate, counting het haploids.
|
|
|
7372 The default is maybefid,maybesid,missphenos,nmiss,nobs,fmiss.
|
|
|
7373 Supported column sets in the variant-based report are:
|
|
|
7374 chrom: Chromosome ID.
|
|
|
7375 pos: Base-pair coordinate.
|
|
|
7376 (ID is always present, and positioned here.)
|
|
|
7377 ref: Reference allele.
|
|
|
7378 alt1: Alternate allele 1.
|
|
|
7379 alt: All alternate alleles, comma-separated.
|
|
|
7380 nmissdosage: Number of missing dosages.
|
|
|
7381 nmiss: Number of missing hardcalls, not counting het haploids.
|
|
|
7382 nmisshh: Number of missing hardcalls, counting het haploids.
|
|
|
7383 hethap: Number of heterozygous haploid calls.
|
|
|
7384 nobs: Number of potentially valid calls.
|
|
|
7385 fmissdosage: Missing dosage rate.
|
|
|
7386 fmiss: Missing hardcall rate, not counting het haploids.
|
|
|
7387 fmisshh: Missing hardcall rate, counting het haploids.
|
|
|
7388 fhethap: Heterozygous haploid rate.
|
|
|
7389 The default is chrom,nmiss,nobs,fmiss.
|
|
|
7390
|
|
|
7391 --hardy ['zs'] ['midp'] ['redundant'] ['cols='<column set descriptor>]
|
|
|
7392 Hardy-Weinberg exact test p-value report(s).
|
|
|
7393 * By default, only founders are considered; change this with --nonfounders.
|
|
|
7394 * chrX is now omitted from the main <output prefix>.hardy report. Instead,
|
|
|
7395 (if present) it gets its own <output prefix>.hardy.x report based on the
|
|
|
7396 method described in Graffelman J, Weir BS (2016) Hardy-Weinberg
|
|
|
7397 equilibrium and the X chromosome.
|
|
|
7398 * For variants with k alleles where k>2, k separate 'biallelic' tests are
|
|
|
7399 performed, each reported on its own line. However, biallelic variants
|
|
|
7400 are normally reported on a single line, since the counts/frequencies
|
|
|
7401 would be mirror-images and the p-values would be the same. You can add
|
|
|
7402 the 'redundant' modifier to force biallelic variant results to be
|
|
|
7403 reported on two lines for parsing convenience.
|
|
|
7404 * There is currently no special handling of case/control phenotypes.
|
|
|
7405 Supported column sets are:
|
|
|
7406 chrom: Chromosome ID.
|
|
|
7407 pos: Base-pair coordinate.
|
|
|
7408 (ID is always present, and positioned here.)
|
|
|
7409 ref: Reference allele.
|
|
|
7410 alt1: Alternate allele 1.
|
|
|
7411 alt: All alternate alleles, comma-separated.
|
|
|
7412 (A1 is always present, and positioned here.)
|
|
|
7413 ax: Non-A1 allele(s), comma-separated.
|
|
|
7414 gcounts: Hom-A1 count, total number of het-A1 calls, and total number of
|
|
|
7415 nonmissing calls with no copies of A1. On chrX, these are
|
|
|
7416 followed by male A1 and male non-A1 counts.
|
|
|
7417 gcount1col: gcounts values in a single comma-separated column.
|
|
|
7418 hetfreq: Observed and expected het-A1 frequencies.
|
|
|
7419 sexaf: Female and male A1 observed allele frequencies (chrX only).
|
|
|
7420 femalep: Female-only p/midp-value (chrX only).
|
|
|
7421 p: Hardy-Weinberg equilibrium exact test p/midp-value.
|
|
|
7422 The default is chrom,ax,gcounts,hetfreq,sexaf,p.
|
|
|
7423
|
|
|
7424 --indep-pairwise <window size>['kb'] [step size (variant ct)]
|
|
|
7425 <unphased-hardcall-r^2 threshold>
|
|
|
7426 Generate a list of variants in approximate linkage equilibrium.
|
|
|
7427 * For multiallelic variants, major allele counts are used in the r^2
|
|
|
7428 computation.
|
|
|
7429 * With the 'kb' modifier, the window size is in kilobase instead of variant
|
|
|
7430 count units. (Pre-'kb' space is optional, i.e.
|
|
|
7431 "--indep-pairwise 500 kb 0.5" and "--indep-pairwise 500kb 0.5" have the
|
|
|
7432 same effect.)
|
|
|
7433 * The step size now defaults to 1 if it's unspecified, and *must* be 1 if
|
|
|
7434 the window is in kilobase units.
|
|
|
7435 * Note that you need to rerun PLINK using --extract or --exclude on the
|
|
|
7436 .prune.in/.prune.out file to apply the list to another computation... and
|
|
|
7437 as with other applications of --extract/--exclude, duplicate variant IDs
|
|
|
7438 are a problem. --indep-pairwise still runs to completion for now when
|
|
|
7439 duplicate variant IDs are present, but that will become an error in alpha
|
|
|
7440 3.
|
|
|
7441
|
|
|
7442 --ld <variant ID> <variant ID> ['dosage'] ['hwe-midp']
|
|
|
7443 This displays diplotype frequencies, r^2, and D' for a single pair of
|
|
|
7444 variants.
|
|
|
7445 * For multiallelic variants, major allele counts/dosages are used.
|
|
|
7446 * Phase information is used when both variants are on the same chromosome.
|
|
|
7447 * When there is at least one sample with unphased het calls for both
|
|
|
7448 variants, diplotype frequencies are estimated using the Hill equation.
|
|
|
7449 If there are multiple biologically possible local maxima, all are
|
|
|
7450 displayed, along with HWE exact test statistics.
|
|
|
7451 * By default, only hardcalls are considered. Add the 'dosage' modifier if
|
|
|
7452 you want dosages to be taken into account. (In the diploid case, an
|
|
|
7453 unphased dosage of x is interpreted as P(0/0) = 1 - x, P(0/1) = x when x
|
|
|
7454 is in 0..1.)
|
|
|
7455
|
|
|
7456 --sample-diff ['id-delim='<char>] ['dosage' | 'dosage='<tolerance>]
|
|
|
7457 ['include-missing'] [{pairwise | counts-only}]
|
|
|
7458 ['fname-id-delim='<c>] ['zs'] ['cols='<column set descriptor>]
|
|
|
7459 ['counts-cols='<column set descriptor>]
|
|
|
7460 {base= | ids=}<sample ID> [other sample ID(s)...]
|
|
|
7461 --sample-diff ['id-delim='<char>] ['dosage' | 'dosage='<tolerance>]
|
|
|
7462 ['include-missing'] [{pairwise | counts-only}]
|
|
|
7463 ['fname-id-delim='<c>] ['zs'] ['cols='<column set descriptor>]
|
|
|
7464 ['counts-cols='<column set descriptor>] file=<ID-pair file>
|
|
|
7465 (alias: --sdiff)
|
|
|
7466 Report discordances and discordance-counts between pairs of samples. If
|
|
|
7467 chrX or chrY is present, sex must be defined and consistent.
|
|
|
7468 * There are three ways to specify which sample pairs to compare. To
|
|
|
7469 compare a single baseline sample against some others, start the
|
|
|
7470 (space-delimited) sample ID list with 'base='. To perform an all-vs.-all
|
|
|
7471 comparison, start it with 'ids=' instead. To compare sample pairs listed
|
|
|
7472 in a file, use 'file='.
|
|
|
7473 Note that 'base='/'ids='/'file=' must be positioned after all modifiers.
|
|
|
7474 * Sample IDs are interpreted as if they were in a VCF header line, with
|
|
|
7475 'id-delim=' having the usual effect.
|
|
|
7476 * By default, comparisons are based on hardcalls. Use 'dosage' to compare
|
|
|
7477 dosages instead; you can combine this with a tolerance in [0, 0.5).
|
|
|
7478 * By default, if one genotype is missing and the other isn't, that doesn't
|
|
|
7479 count as a difference; this can be changed with 'include-missing'.
|
|
|
7480 * By default, a single main report is written to
|
|
|
7481 <output prefix>[.<base ID>].sdiff. To write separate pairwise
|
|
|
7482 <output prefix>.<ID1>.<ID2>.sdiff reports for each compared ID pair, add
|
|
|
7483 the 'pairwise' modifier. To omit the main report, add the 'counts-only'
|
|
|
7484 modifier. (Note that, if you're only interested in nonmissing autosomal
|
|
|
7485 biallelic hardcalls, --make-king-table provides a more efficient way to
|
|
|
7486 compute just counts.)
|
|
|
7487 * By default, if an output filename has a multipart sample ID, the parts
|
|
|
7488 will be delimited by '_'; use 'fname-id-delim=' to change this.
|
|
|
7489 Supported main-report column sets are:
|
|
|
7490 chrom: Chromosome ID.
|
|
|
7491 pos: Base-pair coordinate.
|
|
|
7492 (Variant ID is always present, and positioned here.)
|
|
|
7493 ref: Reference allele.
|
|
|
7494 alt: All alternate alleles, comma-separated.
|
|
|
7495 maybefid: FID1/FID2, if that column was in the input. Requires 'id'.
|
|
|
7496 fid: Force FID1/FID2 even when FID was absent in the input.
|
|
|
7497 id: IID1/IID2.
|
|
|
7498 maybesid: SID1/SID2, if that column was in the input. Requires 'id'.
|
|
|
7499 sid: Force SID1/SID2 even when SID was absent in the input.
|
|
|
7500 geno: Unphased GT or DS for the two samples.
|
|
|
7501 The default is usually chrom,pos,ref,alt,maybefid,id,maybesid,geno; the
|
|
|
7502 sample IDs are removed from the default in 'pairwise' mode.
|
|
|
7503 Supported discordance-count-summary column sets are:
|
|
|
7504 maybefid: FID1/FID2, if that column was in the input.
|
|
|
7505 fid: Force FID1/FID2 even when FID was absent in the input.
|
|
|
7506 (IID1/IID2 are always present.)
|
|
|
7507 maybesid: SID1/SID2, if that column was in the input.
|
|
|
7508 sid: Force SID1/SID2 even when SID was absent in the input.
|
|
|
7509 nobs: Number of variants considered. This includes variants where one or
|
|
|
7510 both variants are missing iff 'include-missing' was specified.
|
|
|
7511 nobsibs: ibs0+ibs1+ibs2.
|
|
|
7512 ibs0: Number of diploid variants with no common hardcall alleles.
|
|
|
7513 ibs1: Number of diploid variants with exactly 1 common hardcall allele.
|
|
|
7514 ibs2: Number of diploid variants with both hardcall alleles matching.
|
|
|
7515 halfmiss: Number of variants with exactly 1 missing genotype/dosage.
|
|
|
7516 Ignored without 'include-missing'.
|
|
|
7517 diff: Total number of differences.
|
|
|
7518 The default is maybefid,maybesid,nobs,halfmiss,diff.
|
|
|
7519
|
|
|
7520 --make-king [{square | square0 | triangle}] [{zs | bin | bin4}]
|
|
|
7521 KING-robust kinship estimator, described by Manichaikul A, Mychaleckyj JC,
|
|
|
7522 Rich SS, Daly K, Sale M, Chen WM (2010) Robust relationship inference in
|
|
|
7523 genome-wide association studies. By default, this writes a
|
|
|
7524 lower-triangular tab-delimited table of kinship coefficients to
|
|
|
7525 <output prefix>.king, and a list of the corresponding sample IDs to
|
|
|
7526 <output prefix>.king.id. The first row of the .king file contains a single
|
|
|
7527 <genome 1-genome 2> kinship coefficient, the second row has the
|
|
|
7528 <genome 1-genome 3> and <genome 2-genome 3> kinship values in that order,
|
|
|
7529 etc.
|
|
|
7530 * Only autosomes are currently considered.
|
|
|
7531 * Pedigree information is currently ignored; the between-family estimator
|
|
|
7532 is used for all pairs.
|
|
|
7533 * For multiallelic variants, REF allele counts are used.
|
|
|
7534 * If the 'square' or 'square0' modifier is present, a square matrix is
|
|
|
7535 written instead; 'square0' fills the upper right triangle with zeroes.
|
|
|
7536 * If the 'zs' modifier is present, the .king file is Zstd-compressed.
|
|
|
7537 * If the 'bin' modifier is present, a binary (square) matrix of
|
|
|
7538 double-precision floating point values, suitable for loading from R, is
|
|
|
7539 instead written to <output prefix>.king.bin. ('bin4' specifies
|
|
|
7540 single-precision numbers instead.) This can be combined with 'square0'
|
|
|
7541 if you still want the upper right zeroed out, or 'triangle' if you don't
|
|
|
7542 want to pad the upper right at all.
|
|
|
7543 * The computation can be subdivided with --parallel.
|
|
|
7544 --make-king-table ['zs'] ['counts'] ['rel-check'] ['cols='<col set descrip.>]
|
|
|
7545 Similar to --make-king, except results are reported in KING's original
|
|
|
7546 .kin0 text table format (with minor changes, e.g. row order is more
|
|
|
7547 friendly to incremental addition of samples), --king-table-filter can be
|
|
|
7548 used to restrict the report to high kinship values, and the 'rel-check'
|
|
|
7549 modifier can be used to restrict to same-FID pairs.
|
|
|
7550 Supported column sets are:
|
|
|
7551 maybefid: FID1/FID2, if that column was in the input. Requires 'id'.
|
|
|
7552 fid: Force FID1/FID2 even when FID was absent in the input.
|
|
|
7553 id: IID1/IID2 (column headers are actually 'ID1'/'ID2' to match KING).
|
|
|
7554 maybesid: SID1/SID2, if that column was in the input. Requires 'id'.
|
|
|
7555 sid: Force SID1/SID2 even when SID was absent in the input.
|
|
|
7556 nsnp: Number of variants considered (autosomal, neither call missing).
|
|
|
7557 hethet: Proportion/count of considered call pairs which are het-het.
|
|
|
7558 ibs0: Proportion/count of considered call pairs which are opposite homs.
|
|
|
7559 ibs1: HET1_HOM2 and HET2_HOM1 proportions/counts.
|
|
|
7560 kinship: KING-robust between-family kinship estimator.
|
|
|
7561 The default is maybefid,id,maybesid,nsnp,hethet,ibs0,kinship.
|
|
|
7562 hethet/ibs0/ibs1 values are proportions unless the 'counts' modifier is
|
|
|
7563 present. If id is omitted, a .kin0.id file is also written.
|
|
|
7564
|
|
|
7565 --make-rel ['cov'] ['meanimpute'] [{square | square0 | triangle}]
|
|
|
7566 [{zs | bin | bin4}]
|
|
|
7567 Write a lower-triangular variance-standardized relationship matrix to
|
|
|
7568 <output prefix>.rel, and corresponding IDs to <output prefix>.rel.id.
|
|
|
7569 * This computation assumes that variants do not have very low MAF, or
|
|
|
7570 deviate greatly from Hardy-Weinberg equilibrium.
|
|
|
7571 * Also, it's usually best to perform this calculation on a variant set in
|
|
|
7572 approximate linkage equilibrium.
|
|
|
7573 * The 'cov' modifier replaces the variance-standardization step with basic
|
|
|
7574 mean-centering, causing a covariance matrix to be calculated instead.
|
|
|
7575 * The computation can be subdivided with --parallel.
|
|
|
7576 --make-grm-list ['cov'] ['meanimpute'] ['zs'] [{id-header | iid-only}]
|
|
|
7577 --make-grm-bin ['cov'] ['meanimpute'] [{id-header | iid-only}]
|
|
|
7578 --make-grm-list causes the relationships to be written to GCTA's original
|
|
|
7579 list format, which describes one pair per line, while --make-grm-bin writes
|
|
|
7580 them in GCTA 1.1+'s single-precision triangular binary format. Note that
|
|
|
7581 these formats explicitly report the number of valid observations (where
|
|
|
7582 neither sample has a missing call) for each pair, which is useful input for
|
|
|
7583 some scripts.
|
|
|
7584
|
|
|
7585 --pca [count] [{approx | meanimpute}] ['scols='<col set descriptor>]
|
|
|
7586 --pca [{biallelic-var-wts | var-wts}] [count] [{approx | meanimpute}] ['vzs']
|
|
|
7587 ['scols='<col set descriptor>] ['vcols='<col set descriptor>]
|
|
|
7588 Extracts top principal components from the variance-standardized
|
|
|
7589 relationship matrix.
|
|
|
7590 * It is usually best to perform this calculation on a variant set in
|
|
|
7591 approximate linkage equilibrium, with no very-low-MAF variants.
|
|
|
7592 * By default, 10 PCs are extracted; you can adjust this by passing a
|
|
|
7593 numeric parameter. (Note that 10 is lower than the PLINK 1.9 default of
|
|
|
7594 20; this is due to the randomized algorithm's memory footprint growing
|
|
|
7595 quadratically w.r.t. the PC count.)
|
|
|
7596 * The 'approx' modifier causes the standard deterministic computation to be
|
|
|
7597 replaced with the randomized algorithm originally implemented for
|
|
|
7598 Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ,
|
|
|
7599 Price AL (2016) Fast Principal-Component Analysis Reveals Convergent
|
|
|
7600 Evolution of ADH1B in Europe and East Asia. This can be a good idea when
|
|
|
7601 you have >5k samples.
|
|
|
7602 * The randomized algorithm always uses mean imputation for missing genotype
|
|
|
7603 calls. For comparison purposes, you can use the 'meanimpute' modifier to
|
|
|
7604 request this behavior for the standard computation.
|
|
|
7605 * 'scols=' can be used to customize how sample IDs appear in the .eigenvec
|
|
|
7606 file. (maybefid, fid, maybesid, and sid supported; default is
|
|
|
7607 maybefid,maybesid.)
|
|
|
7608 * The 'biallelic-var-wts' modifier requests an additional
|
|
|
7609 one-line-per-variant .eigenvec.var file with PCs expressed as variant
|
|
|
7610 weights instead of sample weights, with the condition that all variants
|
|
|
7611 must be biallelic. When it's present, 'vzs' causes the .eigenvec.var
|
|
|
7612 file to be Zstd-compressed.
|
|
|
7613 'vcols=' can be used to customize the report columns; supported column
|
|
|
7614 sets are:
|
|
|
7615 chrom: Chromosome ID.
|
|
|
7616 pos: Base-pair coordinate.
|
|
|
7617 (ID is always present, and positioned here.)
|
|
|
7618 ref: Reference allele.
|
|
|
7619 alt1: Alternate allele 1.
|
|
|
7620 alt: All alternate alleles, comma-separated.
|
|
|
7621 maj: Major allele.
|
|
|
7622 nonmaj: All nonmajor alleles, comma-separated.
|
|
|
7623 (PCs are always present, and positioned here. Signs are w.r.t. the
|
|
|
7624 major, not necessarily reference, allele.)
|
|
|
7625 Default is chrom,maj,nonmaj.
|
|
|
7626 * In this build, 'var-wts' generates the same report as biallelic-var-wts,
|
|
|
7627 except with the "all variants must be biallelic" restriction lifted.
|
|
|
7628 This is temporary. It will no longer be supported as of alpha 3;
|
|
|
7629 instead, there will be an 'allele-wts' mode which seamlessly handles
|
|
|
7630 multiallelic variants, at the cost of generating more verbose
|
|
|
7631 one-line-per-allele output.
|
|
|
7632
|
|
|
7633 --king-cutoff [.king.bin + .king.id fileset prefix] <threshold>
|
|
|
7634 Exclude one member of each pair of samples with KING-robust kinship greater
|
|
|
7635 than the given threshold. Remaining/excluded sample IDs are written to
|
|
|
7636 <output prefix>.king.cutoff.in.id + .king.cutoff.out.id.
|
|
|
7637 If present, the .king.bin file must be triangular (either precision is ok).
|
|
|
7638
|
|
|
7639 --write-covar ['cols='<column set descriptor>]
|
|
|
7640 If covariates are defined, an updated version (with all filters applied) is
|
|
|
7641 automatically written to <output prefix>.cov whenever --make-pgen,
|
|
|
7642 --make-just-psam, --export, or a similar command is present. However, if
|
|
|
7643 you do not wish to simultaneously generate a new sample file, you can use
|
|
|
7644 --write-covar to just produce a pruned covariate file.
|
|
|
7645 Supported column sets are:
|
|
|
7646 maybefid: FID, if that column was in the input.
|
|
|
7647 fid: Force FID column to be written even when absent in the input.
|
|
|
7648 maybesid: SID, if that column was in the input.
|
|
|
7649 sid: Force SID column to be written even when absent in the input.
|
|
|
7650 maybeparents: Father/mother IIDs ('0' = missing), if columns in input.
|
|
|
7651 parents: Force PAT/MAT columns to be written even when absent in input.
|
|
|
7652 sex: '1' = male, '2' = female, 'NA' = missing.
|
|
|
7653 pheno1: First active phenotype. If none, all column entries are set to
|
|
|
7654 the --output-missing-phenotype string.
|
|
|
7655 phenos: All active phenotypes, if any. (Can be combined with pheno1 to
|
|
|
7656 force at least one phenotype column to be written.)
|
|
|
7657 (Covariates are always present, and positioned here.)
|
|
|
7658 The default is maybefid,maybesid.
|
|
|
7659
|
|
|
7660 --write-samples
|
|
|
7661 Report IDs of all samples which pass your filters/inclusion thresholds.
|
|
|
7662
|
|
|
7663 --write-snplist ['zs']
|
|
|
7664 List all variants which pass your filters/inclusion thresholds.
|
|
|
7665
|
|
|
7666 --glm ['zs'] ['omit-ref'] [{sex | no-x-sex}] ['log10'] ['pheno-ids']
|
|
|
7667 [{genotypic | hethom | dominant | recessive}] ['interaction']
|
|
|
7668 ['hide-covar'] ['intercept'] [{no-firth | firth-fallback | firth}]
|
|
|
7669 ['cols='<col set desc.>] ['local-covar='<file>] ['local-pvar='<file>]
|
|
|
7670 ['local-psam='<file>] ['local-omit-last' | 'local-cats='<category ct>]
|
|
|
7671 Basic association analysis on quantitative and/or case/control phenotypes.
|
|
|
7672 For each variant, a linear (for quantitative traits) or logistic (for
|
|
|
7673 case/control) regression is run with the phenotype as the dependent
|
|
|
7674 variable, and nonmajor allele dosage(s) and a constant-1 column as
|
|
|
7675 predictors.
|
|
|
7676 * There is usually an additive effect line for every nonmajor allele, and
|
|
|
7677 no such line for the major allele. To omit REF alleles instead of major
|
|
|
7678 alleles, add the 'omit-ref' modifier. (When performing interaction
|
|
|
7679 testing, this tends to cause the multicollinearity check to fail for
|
|
|
7680 low-ref-frequency variants.)
|
|
|
7681 * By default, sex (male = 1, female = 2; note that this is a change from
|
|
|
7682 PLINK 1.x) is automatically added as a predictor for X chromosome
|
|
|
7683 variants, and no others. The 'sex' modifier causes it to be added
|
|
|
7684 everywhere (except chrY), while 'no-x-sex' excludes it entirely.
|
|
|
7685 * The 'log10' modifier causes p-values to be reported in -log10(p) form.
|
|
|
7686 * 'pheno-ids' causes the samples used in each set of regressions to be
|
|
|
7687 written to an .id file. (When the samples differ on chrX or chrY, .x.id
|
|
|
7688 and/or .y.id files are also written.)
|
|
|
7689 * The 'genotypic' modifier adds an additive effect/dominance deviation 2df
|
|
|
7690 joint test (0-2 and 0..1..0 coding), while 'hethom' uses 0..0..1 and
|
|
|
7691 0..1..0 coding instead.
|
|
|
7692 * 'dominant' and 'recessive' specify a model assuming full dominance or
|
|
|
7693 recessiveness, respectively, for the ref allele. I.e. the genotype
|
|
|
7694 column is recoded as 0..1..1 or 0..0..1, respectively.
|
|
|
7695 * 'interaction' adds genotype x covariate interactions to the model. Note
|
|
|
7696 that this tends to produce 'NA' results (due to the multicollinearity
|
|
|
7697 check) when the reference allele is 'wrong'; --maj-ref can be used to
|
|
|
7698 enable analysis of those variants.
|
|
|
7699 * Additional predictors can be added with --covar. By default, association
|
|
|
7700 statistics are reported for all nonconstant predictors; 'hide-covar'
|
|
|
7701 suppresses covariate-only results, while 'intercept' causes intercepts
|
|
|
7702 to be reported.
|
|
|
7703 * For logistic regression, when the phenotype [quasi-]separates the
|
|
|
7704 genotype, an NA result is currently reported by default. To fall back on
|
|
|
7705 Firth logistic regression instead when the basic logistic regression
|
|
|
7706 fails to converge, add the 'firth-fallback' modifier (highly recommended,
|
|
|
7707 will become the default when beta testing begins). To eliminate the
|
|
|
7708 special case and use Firth logistic regression everywhere, add 'firth'.
|
|
|
7709 'no-firth' can be used to prevent Firth regression from being attempted
|
|
|
7710 in a way that'll still work after alpha testing completes.
|
|
|
7711 * To add covariates which are not constant across all variants, add the
|
|
|
7712 'local-covar=', 'local-pvar=', and 'local-psam=' modifiers, and use full
|
|
|
7713 filenames for each.
|
|
|
7714 Normally, the local-covar file should have c * n real-valued columns,
|
|
|
7715 where the first c columns correspond to the first sample in the
|
|
|
7716 local-psam file, columns (c+1) to 2c correspond to the second sample,
|
|
|
7717 etc.; and the mth line corresponds to the mth nonheader line of the
|
|
|
7718 local-pvar file. (Variants outside of the local-pvar file are excluded
|
|
|
7719 from the regression.) The local covariates are assigned the names
|
|
|
7720 LOCAL1, LOCAL2, etc.; to exclude the last local covariate from the
|
|
|
7721 regression (necessary if they are e.g. local ancestry coefficients which
|
|
|
7722 sum to 1), add 'local-omit-last'.
|
|
|
7723 Alternatively, with 'local-cats='<k>, the local-covar file is expected to
|
|
|
7724 have n columns with integer-valued entries in [1, k]. These category
|
|
|
7725 assignments are expanded into (k-1) local covariates in the usual manner.
|
|
|
7726 The main report supports the following column sets:
|
|
|
7727 chrom: Chromosome ID.
|
|
|
7728 pos: Base-pair coordinate.
|
|
|
7729 (ID is always present, and positioned here.)
|
|
|
7730 ref: Reference allele.
|
|
|
7731 alt1: Alternate allele 1.
|
|
|
7732 alt: All alternate alleles, comma-separated.
|
|
|
7733 (A1 is always present, and positioned here. For multiallelic variants,
|
|
|
7734 this column may contain multiple comma-separated alleles when the result
|
|
|
7735 doesn't depend on which allele is A1.)
|
|
|
7736 ax: Non-A1 alleles, comma-separated.
|
|
|
7737 a1count: A1 allele count (can be decimal with dosage data).
|
|
|
7738 totallele: Allele observation count (can be higher than --freq value, due
|
|
|
7739 to inclusion of het haploids and chrX model).
|
|
|
7740 a1countcc: A1 count in cases, then controls (case/control only).
|
|
|
7741 totallelecc: Case and control allele observation counts.
|
|
|
7742 gcountcc: Genotype hardcall counts (neither-A1, het-A1, A1-A1) in cases,
|
|
|
7743 then controls (case/control only).
|
|
|
7744 a1freq: A1 allele frequency.
|
|
|
7745 a1freqcc: A1 frequency in cases, then controls (case/control only).
|
|
|
7746 machr2: Unphased MaCH imputation quality (frequently labeled 'INFO').
|
|
|
7747 firth: Reports whether Firth regression was used (firth-fallback only).
|
|
|
7748 test: Test identifier. (Required unless only one test is run.)
|
|
|
7749 nobs: Number of samples in the regression.
|
|
|
7750 beta: Regression coefficient (for A1 if additive test).
|
|
|
7751 orbeta: Odds ratio for case/control, beta for quantitative traits.
|
|
|
7752 (Ignored if 'beta' column set included.)
|
|
|
7753 se: Standard error of beta.
|
|
|
7754 ci: Bounds of symmetric approximate confidence interval (requires --ci).
|
|
|
7755 tz: T-statistic for linear regression, Wald Z-score for logistic/Firth.
|
|
|
7756 p: Asymptotic p-value (or -log10(p)) for T/Z-statistic.
|
|
|
7757 err: Error code for NA results.
|
|
|
7758 The default is chrom,pos,ref,alt,firth,test,nobs,orbeta,se,ci,tz,p.
|
|
|
7759
|
|
|
7760 --score <filename> [i] [j] [k] [{header | header-read}]
|
|
|
7761 [{center | variance-standardize | dominant | recessive}]
|
|
|
7762 ['no-mean-imputation'] ['se'] ['zs'] ['ignore-dup-ids']
|
|
|
7763 [{list-variants | list-variants-zs}] ['cols='<col set descriptor>]
|
|
|
7764 Apply linear scoring system(s) to each sample.
|
|
|
7765 The input file should have one line per scored variant. Variant IDs are
|
|
|
7766 read from column #i and allele codes are read from column #j, where i
|
|
|
7767 defaults to 1 and j defaults to i+1. For now, only one allele per
|
|
|
7768 multiallelic variant may be assigned an explicit score; contact us if you
|
|
|
7769 need this changed.
|
|
|
7770 * By default, a single column of input coefficients is read from column #k,
|
|
|
7771 where k defaults to j+1. (--score-col-nums can be used to specify
|
|
|
7772 multiple columns.)
|
|
|
7773 * 'header-read' causes the first line of the input file to be treated as a
|
|
|
7774 header line containing score names. Otherwise, score(s) are assigned the
|
|
|
7775 names 'SCORE1', 'SCORE2', etc.; and 'header' just causes the first line
|
|
|
7776 to be entirely ignored.
|
|
|
7777 * By default, copies of unnamed alleles contribute zero to score, while
|
|
|
7778 missing genotypes contribute an amount proportional to the loaded (via
|
|
|
7779 --read-freq) or imputed allele frequency. To throw out missing
|
|
|
7780 observations instead (decreasing the denominator in the final average
|
|
|
7781 when this happens), use the 'no-mean-imputation' modifier.
|
|
|
7782 * You can use the 'center' modifier to shift all genotypes to mean zero, or
|
|
|
7783 'variance-standardize' to linearly transform the genotypes to mean-0,
|
|
|
7784 variance-1.
|
|
|
7785 * The 'dominant' modifier causes dosages greater than 1 to be treated as 1,
|
|
|
7786 while 'recessive' uses max(dosage - 1, 0) on diploid chromosomes.
|
|
|
7787 ('dominant', 'recessive', and 'variance-standardize' cannot be used with
|
|
|
7788 chrX.)
|
|
|
7789 * The 'se' modifier causes the input coefficients to be treated as
|
|
|
7790 independent standard errors; in this case, standard errors for the score
|
|
|
7791 average/sum are reported. (Note that this will systematically
|
|
|
7792 underestimate standard errors when scored variants are in LD.)
|
|
|
7793 * By default, --score errors out if a variant ID in the input file appears
|
|
|
7794 multiple times in the main dataset. Use the 'ignore-dup-ids' modifier to
|
|
|
7795 skip them instead (a warning is still printed if such variants are
|
|
|
7796 present).
|
|
|
7797 * The 'list-variants[-zs]' modifier causes variant IDs used for scoring to
|
|
|
7798 be written to <output prefix>.sscore.vars[.zst].
|
|
|
7799 The main report supports the following column sets:
|
|
|
7800 maybefid: FID, if that column was in the input.
|
|
|
7801 fid: Force FID column to be written even when absent in the input.
|
|
|
7802 (IID is always present, and positioned here.)
|
|
|
7803 maybesid: SID, if that column was in the input.
|
|
|
7804 sid: Force SID column to be written even when absent in the input.
|
|
|
7805 pheno1: First active phenotype.
|
|
|
7806 phenos: All active phenotypes, if any.
|
|
|
7807 nmissallele: Number of nonmissing alleles.
|
|
|
7808 denom: Denominator of score average (equal to nmissallele value when
|
|
|
7809 'no-mean-imputation' specified).
|
|
|
7810 dosagesum: Sum of named allele dosages.
|
|
|
7811 scoreavgs: Score averages.
|
|
|
7812 scoresums: Score sums.
|
|
|
7813 The default is maybefid,maybesid,phenos,nmissallele,dosagesum,scoreavgs.
|
|
|
7814 For more sophisticated polygenic risk scoring, we recommend the PRSice-2
|
|
|
7815 software package (https://www.prsice.info/ ).
|
|
|
7816
|
|
|
7817 --variant-score <filename> ['zs'] ['bin' | 'cols='<col set descriptor>]
|
|
|
7818 (alias: --vscore)
|
|
|
7819 Apply linear scoring system(s) to each variant. Each reported variant
|
|
|
7820 score is the dot product of a sample-weight vector with the
|
|
|
7821 total-ALT-dosage vector, with MAF-based mean imputation applied to missing
|
|
|
7822 dosages.
|
|
|
7823 Input file format: one line per sample, each starting with an ID and
|
|
|
7824 followed by scoring weight(s); it can also have a header line with the
|
|
|
7825 sample ID representation and the score name(s).
|
|
|
7826 The usual .vscore text report supports the following column sets:
|
|
|
7827 chrom: Chromosome ID.
|
|
|
7828 pos: Base-pair coordinate.
|
|
|
7829 (ID is always present, and positioned here.)
|
|
|
7830 ref: Reference allele.
|
|
|
7831 alt1: Alternate allele 1.
|
|
|
7832 alt: All alternate alleles, comma-separated.
|
|
|
7833 altfreq: ALT allele frequency used for mean-imputation.
|
|
|
7834 nmiss: Number of missing (and thus mean-imputed) dosages.
|
|
|
7835 nobs: Number of (nonmissing) sample observations.
|
|
|
7836 (Variant scores are always present, and positioned here.)
|
|
|
7837 Default is chrom,pos,ref,alt.
|
|
|
7838 If binary output is requested instead, the main .vscore.bin matrix contains
|
|
|
7839 double-precision floating-point values, column (score) ID(s) are saved to a
|
|
|
7840 <output prefix>.vscore.cols, and variant IDs are saved to
|
|
|
7841 <output prefix>.vscore.vars[.zst].
|
|
|
7842
|
|
|
7843 --adjust-file <filename> ['zs'] ['gc'] ['cols='<column set descriptor>]
|
|
|
7844 ['log10'] ['input-log10'] ['test='<test name, case-sensitive>]
|
|
|
7845 Given a file with unfiltered association test results, report some basic
|
|
|
7846 multiple-testing corrections, sorted in increasing-p-value order.
|
|
|
7847 * 'gc' causes genomic-controlled p-values to be used in the formulas.
|
|
|
7848 (This tends to be overly conservative. We note that LD Score regression
|
|
|
7849 usually does a better job of calibrating lambda; see Lee JJ, McGue M,
|
|
|
7850 Iacono WG, Chow CC (2018) The accuracy of LD Score regression as an
|
|
|
7851 estimator of confounding and genetic correlations in genome-wide
|
|
|
7852 association studies.)
|
|
|
7853 * 'log10' causes negative base 10 logs of p-values to be reported, instead
|
|
|
7854 of raw p-values. 'input-log10' specifies that the input file contains
|
|
|
7855 -log10(p) values.
|
|
|
7856 * If the input file contains multiple tests per variant which are
|
|
|
7857 distinguished by a 'TEST' column (true for --linear/--logistic/--glm),
|
|
|
7858 you must use 'test=' to select the test to process.
|
|
|
7859 The following column sets are supported:
|
|
|
7860 chrom: Chromosome ID.
|
|
|
7861 pos: Base-pair coordinate.
|
|
|
7862 (ID is always present, and positioned here.)
|
|
|
7863 ref: Reference allele.
|
|
|
7864 alt1: Alternate allele 1.
|
|
|
7865 alt: All alternate alleles, comma-separated.
|
|
|
7866 a1: Tested allele. (Omitted if missing from input file.)
|
|
|
7867 unadj: Unadjusted p-value.
|
|
|
7868 gc: Devlin & Roeder (1999) genomic control corrected p-value (additive
|
|
|
7869 models only).
|
|
|
7870 qq: P-value quantile.
|
|
|
7871 bonf: Bonferroni correction.
|
|
|
7872 holm: Holm-Bonferroni (1979) adjusted p-value.
|
|
|
7873 sidakss: Sidak single-step adjusted p-value.
|
|
|
7874 sidaksd: Sidak step-down adjusted p-value.
|
|
|
7875 fdrbh: Benjamini & Hochberg (1995) step-up false discovery control.
|
|
|
7876 fdrby: Benjamini & Yekutieli (2001) step-up false discovery control.
|
|
|
7877 Default set is chrom,a1,unadj,gc,bonf,holm,sidakss,sidaksd,fdrbh,fdrby.
|
|
|
7878 --genotyping-rate ['dosage']
|
|
|
7879 Report genotyping rate in log (this was automatic in PLINK 1.x).
|
|
|
7880
|
|
|
7881 --pgen-info
|
|
|
7882 Reports basic information about a .pgen file.
|
|
|
7883
|
|
|
7884 --validate
|
|
|
7885 Validates all variant records in a .pgen file.
|
|
|
7886
|
|
|
7887 --zst-decompress <.zst file> [output filename]
|
|
|
7888 (alias: --zd)
|
|
|
7889 Decompress a Zstd-compressed file. If no output filename is specified, the
|
|
|
7890 file is decompressed to standard output.
|
|
|
7891 This cannot be used with any other flags, and does not cause a log file to
|
|
|
7892 be generated.
|
|
|
7893
|
|
|
7894 The following other flags are supported.
|
|
|
7895 --script <fname> : Include command-line options from file.
|
|
|
7896 --rerun [log] : Rerun commands in log (default 'plink2.log').
|
|
|
7897 --version : Display only version number before exiting.
|
|
|
7898 --silent : Suppress regular output to console. (Error-output is
|
|
|
7899 not suppressed.)
|
|
|
7900 --double-id : Set both FIDs and IIDs to the VCF/.bgen sample ID.
|
|
|
7901 --const-fid [ID] : Set all FIDs to the given constant. If '0' (the
|
|
|
7902 default), no FID column is created.
|
|
|
7903 --id-delim [d] : Normally parses single-delimiter sample IDs as
|
|
|
7904 <FID><d><IID>, and double-delimiter IDs as
|
|
|
7905 <FID><d><IID><d><SID>; default delimiter is '_'.
|
|
|
7906 --id-delim can no longer be used with
|
|
|
7907 --double-id/--const-fid; it will error out if any ID
|
|
|
7908 lacks the delimiter.
|
|
|
7909 --idspace-to <c> : Convert spaces in VCF/.bgen sample IDs to the given
|
|
|
7910 character.
|
|
|
7911 --iid-sid : Make --id-delim and --sample-diff interpret two-token
|
|
|
7912 sample IDs as IID-SID instead of FID-IID.
|
|
|
7913 --vcf-require-gt : Skip variants with no GT field.
|
|
|
7914 --vcf-min-gq <val> : No-call genotypes when GQ is present and below the
|
|
|
7915 threshold.
|
|
|
7916 --vcf-max-dp <val> : No-call genotypes when DP is present and above/below
|
|
|
7917 --vcf-min-dp <val> the threshold.
|
|
|
7918 --vcf-half-call <m> : Specify how '0/.' and similar VCF GT values should be
|
|
|
7919 handled. The following four modes are supported:
|
|
|
7920 * 'error'/'e' (default) errors out and reports line #.
|
|
|
7921 * 'haploid'/'h' treats them as haploid calls.
|
|
|
7922 * 'missing'/'m' treats them as missing.
|
|
|
7923 * 'reference'/'r' treats the missing value as 0.
|
|
|
7924 --oxford-single-chr <chr name> : Specify single-chromosome .gen/.bgen file
|
|
|
7925 with no useful chromosome info inside.
|
|
|
7926 --missing-code [string list] : Comma-delimited list of missing phenotype
|
|
|
7927 (alias: --missing_code) values for Oxford-format import (default
|
|
|
7928 'NA').
|
|
|
7929 --hard-call-threshold <val> : When importing dosage data, a hardcall is
|
|
|
7930 normally saved when the distance from the
|
|
|
7931 nearest hardcall, defined as
|
|
|
7932 0.5 * sum_i |x_i - round(x_i)|
|
|
|
7933 (where the x_i's are 0..2 allele dosages),
|
|
|
7934 is not greater than 0.1. You can adjust
|
|
|
7935 this threshold by providing a numeric
|
|
|
7936 parameter to --hard-call-threshold.
|
|
|
7937 You can also use this with --make-[b]pgen
|
|
|
7938 to alter the saved hardcalls while leaving
|
|
|
7939 the dosages untouched, or --make-bed to
|
|
|
7940 tweak hardcall export.
|
|
|
7941 --dosage-erase-threshold <val> : --hard-call-threshold normally preserves
|
|
|
7942 the original dosages, and several PLINK 2
|
|
|
7943 commands use them when they're available.
|
|
|
7944 Use --dosage-erase-threshold to make PLINK
|
|
|
7945 2 erase dosages and keep only hardcalls
|
|
|
7946 when distance-from-hardcall <= the given
|
|
|
7947 level.
|
|
|
7948 --import-dosage-certainty <val> : The PLINK 2 file format currently supports
|
|
|
7949 a single dosage for each allele. Some
|
|
|
7950 other dosage file formats include a
|
|
|
7951 separate probability for every possible
|
|
|
7952 genotype, e.g. {P(0/0)=0.2, P(0/1)=0.52,
|
|
|
7953 P(1/1)=0.28}, a highly uncertain call that
|
|
|
7954 is nevertheless treated as a hardcall under
|
|
|
7955 '--hard-call-threshold 0.1'. To make PLINK
|
|
|
7956 2 treat a dosage as missing whenever the
|
|
|
7957 largest probability is less than a
|
|
|
7958 threshold, use --import-dosage-certainty.
|
|
|
7959 --input-missing-genotype <c> : '.' is always interpreted as a missing
|
|
|
7960 genotype code in input files. By default, '0'
|
|
|
7961 also is; you can change this second missing
|
|
|
7962 code with --input-missing-genotype.
|
|
|
7963 --allow-extra-chr : Permit unrecognized chromosome codes (alias --aec).
|
|
|
7964 --chr-set <autosome ct> ['no-x'] ['no-y'] ['no-xy'] ['no-mt'] :
|
|
|
7965 Specify a nonhuman chromosome set. The first parameter sets the number of
|
|
|
7966 diploid autosome pairs if positive, or haploid chromosomes if negative.
|
|
|
7967 Given diploid autosomes, the remaining modifiers indicate the absence of
|
|
|
7968 the named non-autosomal chromosomes.
|
|
|
7969 --cow/--dog/--horse/--mouse/--rice/--sheep : Shortcuts for those species.
|
|
|
7970 --autosome-num <val> : Alias for '--chr-set <value> no-y no-xy no-mt'.
|
|
|
7971 --human : Explicitly specify human chromosome set, and make
|
|
|
7972 output .pvar/VCF files include a ##chrSet header
|
|
|
7973 line. (.pvar/VCF output files automatically
|
|
|
7974 include ##chrSet when a nonhuman set is specified.)
|
|
|
7975 --chr-override ['file'] : By default, if --chr-set/--autosome-num/--cow/etc.
|
|
|
7976 conflicts with an input file ##chrSet header line,
|
|
|
7977 PLINK 2 will error out. --chr-override with no
|
|
|
7978 parameter causes the command line to take
|
|
|
7979 precedence; '--chr-override file' defers to the
|
|
|
7980 file.
|
|
|
7981 --var-min-qual <val> : Skip variants with low/missing QUAL.
|
|
|
7982 --var-filter [exception(s)...] : Skip variants which have FILTER failures.
|
|
|
7983 --extract-if-info <key> <op> <val> : Exclude variants which don't/do satisfy
|
|
|
7984 --exclude-if-info <key> <op> <val> a comparison predicate on an INFO key,
|
|
|
7985 (aliases: --extract-if, e.g.
|
|
|
7986 --exclude-if) --extract-if-info "VT == SNP"
|
|
|
7987 Unless the operator is !=, the predicate
|
|
|
7988 always evaluates to false when the key
|
|
|
7989 is missing.
|
|
|
7990 --require-info <key(s)...> : Exclude variants based on nonexistence
|
|
|
7991 --require-no-info <key(s)...> or existence of an INFO key. "<key>=."
|
|
|
7992 is treated as nonexistence.
|
|
|
7993 --extract-col-cond <f> [valcol] [IDcol] [skip] :
|
|
|
7994 --extract-col-cond-match <(sub)string(s)...>
|
|
|
7995 --extract-col-cond-mismatch <(sub)string(s)...>
|
|
|
7996 --extract-col-cond-substr
|
|
|
7997 --extract-col-cond-min <min>
|
|
|
7998 --extract-col-cond-max <max> :
|
|
|
7999 Exclude all variants without a value-column entry satisfying a condition.
|
|
|
8000 * By default, values are read from column 2 of the file, and variant IDs
|
|
|
8001 are read from column 1.
|
|
|
8002 * Three types of conditions are supported:
|
|
|
8003 * When --extract-col-cond-match is specified without
|
|
|
8004 --extract-col-cond-substr, the value is checked for equality with the
|
|
|
8005 given strings, and kept iff one of them matches. Similarly,
|
|
|
8006 --extract-col-cond-mismatch without --extract-col-cond-substr causes
|
|
|
8007 the variant to be kept iff the value matches none of the given strings.
|
|
|
8008 * When --extract-col-cond-match and/or -mismatch are specified with
|
|
|
8009 --extract-col-cond-substr, the variant is kept iff none of the
|
|
|
8010 --extract-col-cond-mismatch substrings are contained in the value, and
|
|
|
8011 either --extract-col-cond-match was unspecified or at least one of its
|
|
|
8012 substrings is contained.
|
|
|
8013 * Otherwise, the value is interpreted as a number, and the variant is
|
|
|
8014 kept if the number is in [<min>, <max>] (default min=0, max=DBL_MAX).
|
|
|
8015 --pheno ['iid-only'] <f> : Specify additional phenotype/covariate file.
|
|
|
8016 Comma-delimited files with a header line are now
|
|
|
8017 permitted.
|
|
|
8018 --pheno-name <name...> : Only load the designated phenotype(s) from the
|
|
|
8019 --pheno (if one was specified) or .psam (if no
|
|
|
8020 --pheno) file. Separate multiple names with
|
|
|
8021 spaces or commas, and use dashes to designate
|
|
|
8022 ranges.
|
|
|
8023 --pheno-col-nums <#...> : Only load the phenotype(s) in the designated
|
|
|
8024 column number(s) from the --pheno file.
|
|
|
8025 --no-psam-pheno : Ignore phenotype(s) in .psam/.fam file.
|
|
|
8026 --strict-sid0 : By default, if there is no SID column in the .psam/.fam
|
|
|
8027 (or --update-ids) file, but there is one in another
|
|
|
8028 input file (for e.g. --keep/--remove), the latter SID
|
|
|
8029 column is ignored; sample IDs are considered matching as
|
|
|
8030 long as FID and IID are equal (with missing FID treated
|
|
|
8031 as '0'). If you also want to require SID = '0' for a
|
|
|
8032 sample ID match in this situation, add --strict-sid0.
|
|
|
8033 --input-missing-phenotype <v> : Set nonzero number to treat as a missing
|
|
|
8034 pheno/covar in input files (default -9).
|
|
|
8035 --no-input-missing-phenotype : Don't treat any nonzero number as a missing
|
|
|
8036 pheno/covar. ('NA'/'nan' are still treated
|
|
|
8037 as missing.)
|
|
|
8038 --1 : Expect case/control phenotypes in input files
|
|
|
8039 to be coded as 0 = control, 1 = case, instead
|
|
|
8040 of the usual 0 = missing, 1 = ctrl, 2 = case.
|
|
|
8041 (Unlike PLINK 1.x, this does not force all
|
|
|
8042 phenotypes to be interpreted as case/ctrl.)
|
|
|
8043 --missing-catname <str> : Set missing-categorical-phenotype string
|
|
|
8044 (case-sensitive, default 'NONE').
|
|
|
8045 --covar ['iid-only'] <f> : Specify additional covariate file.
|
|
|
8046 Comma-delimited files with a header line are now
|
|
|
8047 permitted.
|
|
|
8048 --covar-name <name...> : Only load the designated covariate(s) from the
|
|
|
8049 --covar (if one was specified), --pheno (if no
|
|
|
8050 --covar), or .psam (if no --covar or --pheno)
|
|
|
8051 file.
|
|
|
8052 --covar-col-nums <#...> : Only load the covariate(s) in the designated
|
|
|
8053 column number(s) from the --covar (if one was
|
|
|
8054 specified) or --pheno (if no --covar) file.
|
|
|
8055 --within <f> [new pheno name] : Import a PLINK 1.x categorical phenotype.
|
|
|
8056 (Phenotype name defaults to 'CATPHENO'.)
|
|
|
8057 * If any numeric values are present, ALL
|
|
|
8058 values must be numeric. In that case, 'C'
|
|
|
8059 is added in front of all category names.
|
|
|
8060 * 'NA' is treated as a missing value.
|
|
|
8061 --mwithin <n> : Load --within categories from column n+2.
|
|
|
8062 --family [new pheno name] : Create a categorical phenotype from FID.
|
|
|
8063 Restrictions on and handling of numeric
|
|
|
8064 values are the same as for --within.
|
|
|
8065 --family-missing-catname <nm> : Make --family treat the specified FID as
|
|
|
8066 missing.
|
|
|
8067 --keep <fname...> : Exclude all samples not named in a file.
|
|
|
8068 --remove <fname...> : Exclude all samples named in a file.
|
|
|
8069 --keep-fam <fn...> : Exclude all families not named in a file.
|
|
|
8070 --remove-fam <f...> : Exclude all families named in a file.
|
|
|
8071 --extract [{bed0 | bed1}] <f...> : Usually excludes all variants (not) named
|
|
|
8072 --exclude [{bed0 | bed1}] <f...> in the given file(s). When multiple files
|
|
|
8073 are named, they are concatenated.
|
|
|
8074 With the 'bed0' or 'bed1' modifier,
|
|
|
8075 variants outside/inside the positional
|
|
|
8076 ranges in the interval-BED file(s) are
|
|
|
8077 excluded instead. 'bed0' tells PLINK 2 to
|
|
|
8078 assume the interval bounds follow the UCSC
|
|
|
8079 0-based half-open convention, while 'bed1'
|
|
|
8080 (equivalent to PLINK 1.9 'range')
|
|
|
8081 specifies 1-based fully-closed.
|
|
|
8082 --extract-intersect [{bed0 | bed1}] <f...> : Just like --extract, except that
|
|
|
8083 a variant must be in the
|
|
|
8084 intersection, rather than just
|
|
|
8085 the union, of the files to
|
|
|
8086 remain.
|
|
|
8087 --keep-cats <filename> : These can be used individually or in combination
|
|
|
8088 --keep-cat-names <nm...> to define a list of categories to keep; all
|
|
|
8089 samples not in one of the named categories are
|
|
|
8090 excluded. Use spaces to separate category names
|
|
|
8091 for --keep-cat-names. Use the --missing-catname
|
|
|
8092 value (default 'NONE') to refer to the group of
|
|
|
8093 uncategorized samples.
|
|
|
8094 --keep-cat-pheno <pheno> : If more than one categorical phenotype is loaded,
|
|
|
8095 or you wish to filter on a categorical covariate,
|
|
|
8096 --keep-cat-pheno must be used to specify which
|
|
|
8097 phenotype/covariate --keep-cats and
|
|
|
8098 --keep-cat-names apply to.
|
|
|
8099 --remove-cats <filename> : Exclude all categories named in the file.
|
|
|
8100 --remove-cat-names <...> : Exclude named categories.
|
|
|
8101 --remove-cat-pheno <phe> : Specify pheno for --remove-cats/remove-cat-names.
|
|
|
8102 --split-cat-pheno [{omit-most | omit-last}] ['covar-01']
|
|
|
8103 [cat. pheno/covar name(s)...] :
|
|
|
8104 Split n-category phenotype(s) into n (or n-1, with 'omit-most'/'omit-last')
|
|
|
8105 binary phenotypes, with names of the form <orig. pheno name>=<cat. name>.
|
|
|
8106 (As a consequence, affected phenotypes and categories are not permitted to
|
|
|
8107 contain the '=' character.)
|
|
|
8108 * This happens after all sample filters.
|
|
|
8109 * If no phenotype or covariate names are provided, all categorical
|
|
|
8110 phenotypes (but not covariates) are processed.
|
|
|
8111 * By default, generated covariates are coded as 1=false, 2=true. To code
|
|
|
8112 them as 0=false, 1=true instead, add the 'covar-01' modifier.
|
|
|
8113 --loop-cats <pheno/covar> : Run variant filters and subsequent operations
|
|
|
8114 on just the samples in the first category; then
|
|
|
8115 just the samples in the second category; and so
|
|
|
8116 on, for all categories in the named categorical
|
|
|
8117 phenotype.
|
|
|
8118 --no-id-header ['iid-only'] : Don't include a header line in .id output
|
|
|
8119 files. This normally forces two-column FID/IID
|
|
|
8120 output; add 'iid-only' to force just
|
|
|
8121 single-column IID.
|
|
|
8122 --variance-standardize [pheno/covar name(s)...]
|
|
|
8123 --covar-variance-standardize [covar name(s)...] :
|
|
|
8124 Linearly transform named covariates (and quantitative phenotypes, if
|
|
|
8125 --variance-standardize) to mean-zero, variance 1. If no parameters are
|
|
|
8126 provided, all possible phenotypes/covariates are affected.
|
|
|
8127 This is frequently necessary to prevent multicollinearity when dealing with
|
|
|
8128 covariates where abs(mean) is much larger than abs(standard deviation),
|
|
|
8129 such as year of birth.
|
|
|
8130 --quantile-normalize [...] : Force named covariates and quantitative
|
|
|
8131 --pheno-quantile-normalize [...] phenotypes to a N(0,1) distribution,
|
|
|
8132 --covar-quantile-normalize [...] preserving only the original rank orders.
|
|
|
8133 --chr <chr(s)...> : Exclude all variants not on the given chromosome(s).
|
|
|
8134 Valid choices for humans are 0 (unplaced), 1-22, X, Y,
|
|
|
8135 XY, MT, PAR1, and PAR2. Separate multiple chromosomes
|
|
|
8136 with spaces and/or commas, and use a dash (no adjacent
|
|
|
8137 spaces permitted) to denote a range, e.g.
|
|
|
8138 '--chr 1-4, 22, par1, x, par2'.
|
|
|
8139 --not-chr <...> : Reverse of --chr (exclude variants on listed
|
|
|
8140 chromosomes).
|
|
|
8141 --autosome : Exclude all non-autosomal variants.
|
|
|
8142 --autosome-par : Exclude all non-autosomal variants, except those in a
|
|
|
8143 pseudo-autosomal region.
|
|
|
8144 --snps-only ['just-acgt'] : Exclude non-SNP variants. By default, SNP = all
|
|
|
8145 allele codes are single-character (so
|
|
|
8146 multiallelic variants with a mix of SNPs and
|
|
|
8147 non-SNPs are excluded; split your variants first
|
|
|
8148 if that's a problem).
|
|
|
8149 The 'just-acgt' modifier restricts SNP codes to
|
|
|
8150 {A,C,G,T,a,c,g,t,<missing>}.
|
|
|
8151 --from <var ID> : Use ID(s) to specify a variant range to load. When used
|
|
|
8152 --to <var ID> together, both variants must be on the same chromosome.
|
|
|
8153 (--snps can be used to specify intervals which cross
|
|
|
8154 chromosome boundaries.)
|
|
|
8155 --snp <var ID> : Specify a single variant to load.
|
|
|
8156 --exclude-snp <ID> : Specify a single variant to exclude.
|
|
|
8157 --window <kbs> : With --snp/--exclude-snp, loads/excludes all variants
|
|
|
8158 within half the specified kb distance of the named one.
|
|
|
8159 --from-bp <pos> : Use base-pair coordinates to define a variant range to
|
|
|
8160 --to-bp <pos> load.
|
|
|
8161 --from-kb <pos> * You must use these with --chr, specifying a single
|
|
|
8162 --to-kb <pos> chromosome.
|
|
|
8163 --from-mb <pos> * Decimals and negative numbers are permitted.
|
|
|
8164 --to-mb <pos> * The --to-bp(/-kb/-mb) position is no longer permitted
|
|
|
8165 to be smaller than the --from-bp position.
|
|
|
8166 --snps <var IDs...> : Use IDs to specify variant range(s) to load or
|
|
|
8167 --exclude-snps <...> exclude. E.g. '--snps rs1111-rs2222, rs3333, rs4444'.
|
|
|
8168 --force-intersect : PLINK 2 normally errors out when multiple variant
|
|
|
8169 inclusion filters (--extract, --extract-col-cond,
|
|
|
8170 --extract-intersect, --from/--to, --from-bp/--to-bp,
|
|
|
8171 --snp, --snps) are specified. --force-intersect
|
|
|
8172 allows the run to proceed; the set intersection will
|
|
|
8173 be taken.
|
|
|
8174 --thin <p> : Randomly remove variants, retaining each with prob. p.
|
|
|
8175 --thin-count <n> : Randomly remove variants until n of them remain.
|
|
|
8176 --bp-space <bps> : Remove variants so that each pair is no closer than
|
|
|
8177 the given bp distance.
|
|
|
8178 --thin-indiv <p> : Randomly remove samples, retaining with prob. p.
|
|
|
8179 --thin-indiv-count <n> : Randomly remove samples until n of them remain.
|
|
|
8180 --keep-col-match <f> <val(s)...> : Exclude all samples without a 3rd column
|
|
|
8181 entry in the given file exactly matching
|
|
|
8182 one of the given strings. (Separate
|
|
|
8183 multiple strings with spaces.)
|
|
|
8184 --keep-col-match-name <col name> : Check column with given name instead.
|
|
|
8185 --keep-col-match-num <n> : Check nth column instead.
|
|
|
8186 --geno [val] [{dosage | hh-missing}]
|
|
|
8187 --mind [val] [{dosage | hh-missing}] :
|
|
|
8188 Exclude variants (--geno) and/or samples (--mind) with missing call
|
|
|
8189 frequencies greater than a threshold (default 0.1). (Note that the default
|
|
|
8190 threshold is only applied if --geno/--mind is invoked without a parameter;
|
|
|
8191 when --geno/--mind is not invoked, no missing call frequency ceiling is
|
|
|
8192 enforced at all. Other inclusion/exclusion default thresholds work the
|
|
|
8193 same way.)
|
|
|
8194 By default, when a dosage is present but a hardcall is not, the genotype is
|
|
|
8195 treated as missing; add the 'dosage' modifier to treat this case as
|
|
|
8196 nonmissing. Alternatively, you can use 'hh-missing' to also treat
|
|
|
8197 heterozygous haploid calls as missing.
|
|
|
8198 --require-pheno [name(s)...] : Remove samples missing any of the named
|
|
|
8199 --require-covar [name(s)...] phenotype(s)/covariate(s). If no parameters
|
|
|
8200 are provided, all phenotype(s)/covariate(s)
|
|
|
8201 must be present.
|
|
|
8202 --maf [freq] [mode] : Exclude variants with allele frequency lower than a
|
|
|
8203 (alias: --min-af) threshold (default 0.01). By default, the nonmajor
|
|
|
8204 allele frequency is used; the other supported modes
|
|
|
8205 are 'nref' (non-reference), 'alt1', and 'minor'
|
|
|
8206 (least frequent). bcftools freq:mode notation is
|
|
|
8207 permitted.
|
|
|
8208 --max-maf <freq> [mode] : Exclude variants with MAF greater than the
|
|
|
8209 (alias: --max-af) threshold.
|
|
|
8210 --mac <ct> [mode] : Exclude variants with allele dosage lower than the
|
|
|
8211 (alias: --min-ac) given threshold.
|
|
|
8212 --max-mac <ct> [mode] : Exclude variants with allele dosage greater than
|
|
|
8213 (alias: --max-ac) the given threshold.
|
|
|
8214 --maf-succ : Rule of succession allele frequency estimation (used in
|
|
|
8215 EIGENSOFT). Given j observations of one allele and k
|
|
|
8216 observations of the other for a biallelic variant, infer
|
|
|
8217 allele frequencies of (j+1) / (j+k+2) and
|
|
|
8218 (k+1) / (j+k+2), rather than the default j / (j+k) and
|
|
|
8219 k / (j+k).
|
|
|
8220 Note that this does not affect --freq's output.
|
|
|
8221 --min-alleles <ct> : Exclude variants with fewer than the given # of alleles.
|
|
|
8222 (When a variant has exactly one ALT allele, and it's
|
|
|
8223 a missing-code, it's excluded by "--min-alleles 2".)
|
|
|
8224 --max-alleles <ct> : Exclude variants with more than the given # of alleles.
|
|
|
8225 --read-freq <file> : Load allele frequency estimates from the given --freq or
|
|
|
8226 --geno-counts (or PLINK 1.9 --freqx) report, instead of
|
|
|
8227 imputing them from the immediate dataset.
|
|
|
8228 --hwe <p> ['midp'] ['keep-fewhet'] :
|
|
|
8229 Exclude variants with Hardy-Weinberg equilibrium exact test p-values below
|
|
|
8230 a threshold.
|
|
|
8231 * By default, only founders are considered.
|
|
|
8232 * chrX p-values are now computed using Graffelman and Weir's method.
|
|
|
8233 * For variants with k alleles with k>2, k separate 'biallelic' tests are
|
|
|
8234 performed, and the variant is filtered out if any of them fail.
|
|
|
8235 * With 'keep-fewhet', variants which fail the test in the too-few-hets
|
|
|
8236 direction are not excluded. On chrX, this uses the ratio between the
|
|
|
8237 Graffelman/Weir p-value and the female-only p-value.
|
|
|
8238 * There is currently no special handling of case/control phenotypes.
|
|
|
8239 --mach-r2-filter [min] [max] : Exclude variants with MaCH imputation quality
|
|
|
8240 metric less than min or greater than max
|
|
|
8241 (defaults 0.1 and 2.0). (Monomorphic
|
|
|
8242 variants, with r2 = nan, are not excluded.)
|
|
|
8243 * This is NOT identical to the R2 metric
|
|
|
8244 reported by Minimac3 0.1.13+; see below.
|
|
|
8245 * If a single parameter is provided, it is
|
|
|
8246 treated as the minimum.
|
|
|
8247 * The metric is not computed on chrX and MT.
|
|
|
8248 --minimac3-r2-filter <min> [max] : Compute Minimac3 R2 values from scratch,
|
|
|
8249 and exclude variants with R2 less than min
|
|
|
8250 or (if max is provided) greater than max.
|
|
|
8251 * Note that this requires phased-dosage
|
|
|
8252 data for all samples and variants;
|
|
|
8253 otherwise this will systematically
|
|
|
8254 underestimate imputation quality, since
|
|
|
8255 unphased hardcalls/dosages are treated
|
|
|
8256 as if they were maximally uncertain.
|
|
|
8257 (Use --extract-if-info/--exclude-if-info
|
|
|
8258 to filter on precomputed Minimac3 R2 in
|
|
|
8259 a VCF/.pvar INFO column.)
|
|
|
8260 --keep-females : Exclude male and unknown-sex samples.
|
|
|
8261 --keep-males : Exclude female and unknown-sex samples.
|
|
|
8262 --keep-nosex : Exclude all known-sex samples.
|
|
|
8263 --remove-females : Exclude female samples.
|
|
|
8264 --remove-males : Exclude male samples.
|
|
|
8265 --remove-nosex : Exclude unknown-sex samples.
|
|
|
8266 --keep-founders : Exclude nonfounder samples.
|
|
|
8267 --keep-nonfounders : Exclude founder samples.
|
|
|
8268 --keep-if <pheno/covar> <op> <val> : Exclude samples which don't/do satisfy a
|
|
|
8269 --remove-if <pheno/covar> <op> <v> comparison predicate, e.g.
|
|
|
8270 --keep-if "PHENO1 == case"
|
|
|
8271 Unless the operator is !=, the predicate
|
|
|
8272 always evaluates to false when the
|
|
|
8273 phenotype/covariate is missing.
|
|
|
8274 --nonfounders : Include nonfounders in allele freq/HWE calculations.
|
|
|
8275 --bad-freqs : When PLINK 2 needs decent allele frequencies, it
|
|
|
8276 normally errors out if they aren't provided by
|
|
|
8277 --read-freq and less than 50 founders are available to
|
|
|
8278 impute them from. Use --bad-freqs to force PLINK 2 to
|
|
|
8279 proceed in this case.
|
|
|
8280 --export-allele <file> : With --export A/A-transpose/AD, count alleles named
|
|
|
8281 in the file, instead of REF alleles.
|
|
|
8282 --output-chr <MT code> : Set chromosome coding scheme in output files by
|
|
|
8283 providing the desired human mitochondrial code.
|
|
|
8284 Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM',
|
|
|
8285 and 'chrMT'; default is now 'MT' (note that this is
|
|
|
8286 a change from PLINK 1.x, which defaulted to '26').
|
|
|
8287 --output-missing-genotype <ch> : Set the code used to represent missing
|
|
|
8288 genotypes in output files (default '.').
|
|
|
8289 --output-missing-phenotype <s> : Set the string used to represent missing
|
|
|
8290 phenotypes in output files (default 'NA').
|
|
|
8291 --sort-vars [mode] : Sort variants by chromosome, then position, then
|
|
|
8292 ID. The following string orders are supported:
|
|
|
8293 * 'natural'/'n': Natural sort (default).
|
|
|
8294 * 'ascii'/'a': ASCII.
|
|
|
8295 This must be used with --make-[b]pgen/--make-bed.
|
|
|
8296 --set-hh-missing ['keep-dosage'] : Make --make-[b]pgen/--make-bed set non-MT
|
|
|
8297 heterozygous haploid hardcalls, and all
|
|
|
8298 female chrY calls, to missing. (Unlike
|
|
|
8299 PLINK 1.x, this treats unknown-sex chrY
|
|
|
8300 genotypes like males, not females.)
|
|
|
8301 By default, all associated dosages are
|
|
|
8302 also erased; use 'keep-dosage' to keep
|
|
|
8303 them all.
|
|
|
8304 --set-mixed-mt-missing ['keep-dosage'] : Make --make-[b]pgen/--make-bed set
|
|
|
8305 mixed MT hardcalls to missing.
|
|
|
8306 --split-par <bp1> <bp2> : Changes chromosome code of all X chromosome
|
|
|
8307 --split-par <build> variants with bp position <= bp1 to PAR1, and those
|
|
|
8308 with position >= bp2 to PAR2. The following build
|
|
|
8309 codes are supported as shorthand:
|
|
|
8310 * 'b36'/'hg18' = NCBI 36, 2709521/154584237
|
|
|
8311 * 'b37'/'hg19' = GRCh37, 2699520/154931044
|
|
|
8312 * 'b38'/'hg38' = GRCh38, 2781479/155701383
|
|
|
8313 --merge-par : Merge PAR1/PAR2 back with X. Requires PAR1 to be
|
|
|
8314 positioned immediately before X, and PAR2 to be
|
|
|
8315 immediately after X. (Should *not* be used with
|
|
|
8316 "--export vcf", since it causes male
|
|
|
8317 homozygous/missing calls in PAR1/PAR2 to be
|
|
|
8318 reported as haploid.)
|
|
|
8319 --merge-x : Merge XY back with X. This usually has to be
|
|
|
8320 combined with --sort-vars.
|
|
|
8321 --set-missing-var-ids <t> : Given a template string with a '@' where the
|
|
|
8322 --set-all-var-ids <t> chromosome code should go and '#' where the bp
|
|
|
8323 coordinate belongs, --set-missing-var-ids
|
|
|
8324 assigns chromosome-and-bp-based IDs to unnamed
|
|
|
8325 variants, while --set-all-var-ids resets all
|
|
|
8326 IDs.
|
|
|
8327 You may also use '$r'/'$a' to refer to the
|
|
|
8328 ref and alt1 alleles, or '$1'/'$2' to refer to
|
|
|
8329 them in alphabetical order.
|
|
|
8330 --var-id-multi <t> : Specify alternative templates for multiallelic
|
|
|
8331 --var-id-multi-nonsnp <t> variants. ('$a' and '$1'/'$2' should be avoided
|
|
|
8332 here, though they're technically still allowed.)
|
|
|
8333 --new-id-max-allele-len <len> [{error | missing | truncate}] :
|
|
|
8334 Specify maximum number of leading characters from allele codes to include
|
|
|
8335 in new variant IDs, and behavior on longer codes (defaults 23, error).
|
|
|
8336 --missing-var-code <str> : Change unnamed variant code for --rm-dup,
|
|
|
8337 --set-{missing|all}-var-ids, and
|
|
|
8338 --recover-var-ids (default '.').
|
|
|
8339 --update-map <f> [bpcol] [IDcol] [skip] : Update variant bp positions.
|
|
|
8340 --update-name <f> [newcol] [oldcol] [skip] : Update variant IDs.
|
|
|
8341 --recover-var-ids <file> ['strict-bim-order'] [{rigid | force}] ['partial'] :
|
|
|
8342 Undo --set-all-var-ids, given the original .pvar/VCF/.bim file. Original
|
|
|
8343 IDs are looked up by position and allele codes.
|
|
|
8344 * By default, if the original-ID file is a .bim, allele order is ignored.
|
|
|
8345 Use 'strict-bim-order' to force A1=ALT, A2=REF.
|
|
|
8346 * If any variant has multiple matching records in the original-ID file, and
|
|
|
8347 the IDs conflict, --recover-var-ids writes the affected (current) ID(s)
|
|
|
8348 to <output prefix>.recoverid.dup, and normally errors out. If the
|
|
|
8349 original-ID file has the same number of variants in the same order, you
|
|
|
8350 can still recover the old IDs with the 'rigid' modifier in this case.
|
|
|
8351 Alternatively, to proceed and assign the missing-ID code to these
|
|
|
8352 variants, add the 'force' modifier. (The .recoverid.dup file is still
|
|
|
8353 written when 'rigid' or 'force' is specified.)
|
|
|
8354 * --recover-var-ids normally expects to replace all variant IDs, and errors
|
|
|
8355 out if any are left untouched. Add the 'partial' modifier when you
|
|
|
8356 actually want to update just a proper subset.
|
|
|
8357 --update-alleles <fname> : Update variant allele codes.
|
|
|
8358 --update-ids <fname> : Update sample IDs.
|
|
|
8359 --update-parents <fname> : Update parental IDs.
|
|
|
8360 --update-sex <filename> ['col-num='<n>] ['male0'] :
|
|
|
8361 Update sex information.
|
|
|
8362 * By default, if there is a header line starting with '#FID'/'#IID', sex is
|
|
|
8363 loaded from the first column titled 'SEX' (any capitalization);
|
|
|
8364 otherwise, column 3 is assumed. Use 'col-num=' to force a column number.
|
|
|
8365 * Only the first character in the sex column is processed. By default,
|
|
|
8366 '1'/'M'/'m' is interpreted as male, '2'/'F'/'f' is interpreted as female,
|
|
|
8367 and '0'/'N' is interpreted as unknown-sex. To change this to '0'/'M'/'m'
|
|
|
8368 = male, '1'/'F'/'f' = female, anything else other than '2' = unknown-sex,
|
|
|
8369 add 'male0'.
|
|
|
8370 --real-ref-alleles : Treat A2 alleles in a PLINK 1.x fileset as actual REF
|
|
|
8371 alleles; otherwise they're marked as provisional.
|
|
|
8372 --maj-ref ['force'] : Set major alleles to reference, like PLINK 1.x
|
|
|
8373 automatically did. (Note that this is now opt-in
|
|
|
8374 rather than opt-out; --keep-allele-order is no longer
|
|
|
8375 necessary to prevent allele-swapping.)
|
|
|
8376 * This can only be used in runs with
|
|
|
8377 --make-bed/--make-[b]pgen/--export and no other
|
|
|
8378 commands.
|
|
|
8379 * By default, this only affects variants marked as
|
|
|
8380 having 'provisional' reference alleles. Add 'force'
|
|
|
8381 to apply this to all variants.
|
|
|
8382 * All new reference alleles are marked as provisional.
|
|
|
8383 --ref-allele ['force'] <filename> [refcol] [IDcol] [skip]
|
|
|
8384 --alt1-allele ['force'] <filename> [alt1col] [IDcol] [skip] :
|
|
|
8385 These set the alleles specified in the file to ref (--ref-allele) or alt1
|
|
|
8386 (--alt1-allele). They can be combined in the same run.
|
|
|
8387 * These can only be used in runs with --make-bed/--make-[b]pgen/--export
|
|
|
8388 and no other commands.
|
|
|
8389 * "--ref-allele <VCF filename> 4 3 '#'", which scrapes reference allele
|
|
|
8390 assignments from a VCF file, is especially useful.
|
|
|
8391 * By default, these error out when asked to change a 'known' reference
|
|
|
8392 allele. Add 'force' to permit that (when e.g. switching to a new
|
|
|
8393 reference genome).
|
|
|
8394 * When --alt1-allele changes the previous ref allele to alt1, the previous
|
|
|
8395 alt1 allele is set to reference and marked as provisional.
|
|
|
8396 --ref-from-fa ['force'] : This sets reference alleles from the --fa file when
|
|
|
8397 it can be done unambiguously (note that it's never
|
|
|
8398 possible for deletions or some insertions).
|
|
|
8399 By default, it errors out when asked to change a
|
|
|
8400 'known' reference allele; add the 'force' modifier
|
|
|
8401 to permit that.
|
|
|
8402 --normalize ['list'] : Left-normalize all variants, using the --fa file.
|
|
|
8403 (alias: --norm) (Assumes no differences in capitalization.) The
|
|
|
8404 'list' modifier causes a list of affected variant
|
|
|
8405 IDs to be written to <output prefix>.normalized.
|
|
|
8406 --indiv-sort <mode> [f] : Specify sample ID sort order for merge and
|
|
|
8407 --make-[b]pgen/--make-bed. The following four
|
|
|
8408 modes are supported:
|
|
|
8409 * 'none'/'0' keeps samples in the order they were
|
|
|
8410 loaded. Default for non-merge.
|
|
|
8411 * 'natural'/'n' invokes "natural sort", e.g.
|
|
|
8412 'id2' < 'ID3' < 'id10'. Default when merging.
|
|
|
8413 * 'ascii'/'a' sorts in ASCII order, e.g.
|
|
|
8414 'ID3' < 'id10' < 'id2'.
|
|
|
8415 * 'file'/'f' uses the order in the given file
|
|
|
8416 (named in the last parameter).
|
|
|
8417 --king-table-filter <min> : Specify minimum kinship coefficient for
|
|
|
8418 inclusion in --make-king-table report.
|
|
|
8419 --king-table-subset <f> [kmin] : Restrict current --make-king-table run to
|
|
|
8420 sample pairs listed in the given .kin0 file.
|
|
|
8421 If a second parameter is provided, only
|
|
|
8422 sample pairs with kinship >= that threshold
|
|
|
8423 (in the input .kin0) are processed.
|
|
|
8424 --condition <variant ID> [{dominant | recessive}] ['multiallelic']
|
|
|
8425 --condition-list <fname> [{dominant | recessive}] ['multiallelic'] :
|
|
|
8426 Add the given variant, or all variants in the given file, as --glm
|
|
|
8427 covariates.
|
|
|
8428 By default, this errors out if any of the variants are multiallelic; add
|
|
|
8429 the 'multiallelic' ('m' for short) modifier to allow them. They'll
|
|
|
8430 effectively be split against the major allele (unless --glm's 'omit-ref'
|
|
|
8431 modifier was specified), and all induced covariate names--even for
|
|
|
8432 biallelic variants--will have an underscore followed by the allele code at
|
|
|
8433 the end.
|
|
|
8434 --parameters <...> : Include only the given covariates/interactions in the
|
|
|
8435 --glm model, identified by a list of 1-based indices
|
|
|
8436 and/or ranges of them.
|
|
|
8437 --tests <...> : Perform a (joint) test on the specified term(s) in the
|
|
|
8438 --tests all --glm model, identified by 1-based indices and/or ranges
|
|
|
8439 of them.
|
|
|
8440 * Note that, when --parameters is also present, the
|
|
|
8441 indices refer to the terms remaining AFTER pruning by
|
|
|
8442 --parameters.
|
|
|
8443 * You can use '--tests all' to include all terms.
|
|
|
8444 --vif <max VIF> : Set VIF threshold for --glm multicollinearity check
|
|
|
8445 (default 50). (This is no longer skipped for
|
|
|
8446 case/control phenotypes.)
|
|
|
8447 --max-corr <val> : Skip --glm regression when the absolute value of the
|
|
|
8448 correlation between two predictors exceeds this value
|
|
|
8449 (default 0.999).
|
|
|
8450 --xchr-model <m> : Set the chrX --glm/--condition[-list]/--[v]score model.
|
|
|
8451 * '0' = skip chrX.
|
|
|
8452 * '1' = add sex as a covar on chrX, code males 0..1.
|
|
|
8453 * '2' (default) = chrX sex covar, code males 0..2.
|
|
|
8454 (Use the --glm 'interaction' modifier to test for
|
|
|
8455 interaction between genotype and sex.)
|
|
|
8456 --adjust ['zs'] ['gc'] ['log10'] ['cols='<column set descriptor>] :
|
|
|
8457 For each association test in this run, report some basic multiple-testing
|
|
|
8458 corrections, sorted in increasing-p-value order. Modifiers work the same
|
|
|
8459 way as they do on --adjust-file.
|
|
|
8460 --lambda : Set genomic control lambda for --adjust[-file].
|
|
|
8461 --adjust-chr-field <n...> : Set --adjust-file input field names. When
|
|
|
8462 --adjust-pos-field <n...> multiple parameters are given to these flags,
|
|
|
8463 --adjust-id-field <n...> earlier names take precedence over later ones.
|
|
|
8464 --adjust-ref-field <n...>
|
|
|
8465 --adjust-alt-field <n...>
|
|
|
8466 --adjust-a1-field <n...>
|
|
|
8467 --adjust-test-field <n...>
|
|
|
8468 --adjust-p-field <n...>
|
|
|
8469 --ci <size> : Report confidence ratios for odds ratios/betas.
|
|
|
8470 --pfilter <val> : Filter out assoc. test results with higher p-values.
|
|
|
8471 --score-col-nums <...> : Process all the specified coefficient columns in the
|
|
|
8472 --score file, identified by 1-based indexes and/or
|
|
|
8473 ranges of them.
|
|
|
8474 --q-score-range <range file> <data file> [i] [j] ['header'] ['min'] :
|
|
|
8475 Apply --score to subset(s) of variants in the primary score list(s) based
|
|
|
8476 on e.g. p-value ranges.
|
|
|
8477 * The first file should have range labels in the first column, p-value
|
|
|
8478 lower bounds in the second column, and upper bounds in the third column.
|
|
|
8479 Lines with too few entries, or nonnumeric values in the second or third
|
|
|
8480 column, are ignored.
|
|
|
8481 * The second file should contain a variant ID and a p-value on each line
|
|
|
8482 (except possibly the first). Variant IDs are read from column #i and
|
|
|
8483 p-values are read from column #j, where i defaults to 1 and j defaults to
|
|
|
8484 i+1. The 'header' modifier causes the first nonempty line of this file
|
|
|
8485 to be skipped.
|
|
|
8486 * By default, --q-score-range errors out when a variant ID appears multiple
|
|
|
8487 times in the data file (and is also present in the main dataset). To use
|
|
|
8488 the minimum p-value in this case instead, add the 'min' modifier.
|
|
|
8489 --vscore-col-nums <...> : Process all the specified coefficient columns in
|
|
|
8490 the --variant-score file, identified by 1-based
|
|
|
8491 indexes and/or ranges of them.
|
|
|
8492 --parallel <k> <n> : Divide the output matrix into n pieces, and only compute
|
|
|
8493 the kth piece. The primary output file will have the
|
|
|
8494 piece number included in its name, e.g. plink2.king.13
|
|
|
8495 or plink2.king.13.zst if k is 13. Concatenating these
|
|
|
8496 files in order will yield the full matrix of interest.
|
|
|
8497 (Yes, this can be done before decompression.)
|
|
|
8498 N.B. This generally cannot be used to directly write a
|
|
|
8499 symmetric square matrix. Choose square0 or triangle
|
|
|
8500 shape instead, and postprocess as necessary.
|
|
|
8501 --memory <val> ['require'] : Set size, in MiB, of initial workspace malloc
|
|
|
8502 attempt. To error out instead of reducing the
|
|
|
8503 request size when the initial attempt fails, add
|
|
|
8504 the 'require' modifier.
|
|
|
8505 --threads <val> : Set maximum number of compute threads.
|
|
|
8506 --d <char> : Change variant/covariate range delimiter (normally '-').
|
|
|
8507 --seed <val...> : Set random number seed(s). Each value must be an
|
|
|
8508 integer between 0 and 4294967295 inclusive.
|
|
|
8509 Note that --threads and "--memory require" may also be
|
|
|
8510 needed to reproduce some randomized runs.
|
|
|
8511 --output-min-p <p> : Specify minimum p-value to write to reports. (2.23e-308
|
|
|
8512 is useful for preventing underflow in some programs.)
|
|
|
8513 --debug : Use slower, more crash-resistant logging method.
|
|
|
8514 --randmem : Randomize initial workspace memory (helps catch
|
|
|
8515 uninitialized-memory bugs).
|
|
|
8516 --warning-errcode : Return a nonzero error code to the OS when a run
|
|
|
8517 completes with warning(s).
|
|
|
8518 --zst-level <lvl> : Set the Zstd compression level (1-22, default 3).
|
|
|
8519
|
|
|
8520 Primary methods paper:
|
|
|
8521 Chang CC, Chow CC, Tellier LCAM, Vattikuti S, Purcell SM, Lee JJ (2015)
|
|
|
8522 Second-generation PLINK: rising to the challenge of larger and richer datasets.
|
|
|
8523 GigaScience, 4.
|
|
|
8524
|
|
|
8525
|
|
|
8526
|
|
|
8527 ]]></help>
|
|
|
8528 <citations>
|
|
|
8529 <citation type="doi">10.1186/s13742-015-0047-8</citation>
|
|
|
8530 <citation type="bibtex">@ARTICLE{Blankenberg20-plink,
|
|
|
8531 author = {Daniel Blankenberg Lab, et al},
|
|
|
8532 title = {In preparation..},
|
|
|
8533 }</citation>
|
|
|
8534 </citations>
|
|
|
8535 </tool>
|
