Mercurial > repos > iuc > bcftools_stats

annotate bcftools_stats.xml @ 8:96fe8635d07d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author iuc
date Thu, 21 Feb 2019 15:26:13 -0500
parents 64db9662b6b3
children 70b4263bae27
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
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3 <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">stats</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements">
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9 <expand macro="samtools_requirement"/>
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10 <requirement type="package" version="3.0.2">matplotlib</requirement>
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11 <requirement type="package" version="0.1.11">tectonic</requirement>
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12 </expand>
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13 <expand macro="version_command" />
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14 <command detect_errors="aggressive"><![CDATA[
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15 @PREPARE_ENV@
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16 #set $input_files = [$input_file]
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17 #if $inputB_file:
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18 #silent $input_files.append($inputB_file)
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19 #end if
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20 @PREPARE_INPUT_FILES@
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21 #set $section = $sec_restrict
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22 @PREPARE_TARGETS_FILE@
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23 @PREPARE_REGIONS_FILE@
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24 ## Stats section
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25 #set $section = $sec_default
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26 @PREPARE_FASTA_REF@
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27 @PREPARE_EXONS_FILE@
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29 bcftools @EXECUTABLE@
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30
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31 ## Stats section
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32 #set $section = $sec_default
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33 @FASTA_REF@
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34 @EXONS_FILE@
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35 ${section.first_allele_only}
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36 #if $section.depth.set_depth == 'yes':
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37 --depth ${section.depth.depth_min},${section.depth.depth_max},${section.depth.depth_bin_size}
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38 #end if
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39 #if $section.user_tstv:
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40 --user-tstv '${section.user_tstv}'
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41 #end if
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42 #if $section.afbins.afbins_select == 'af_bins_list':
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43 --af-bins '$section.afbins.af_bins_list'
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44 #elif $section.afbins.afbins_select == 'af_bins_file':
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45 --af-bins '$section.afbins.af_bins_file'
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46 #end if
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47 #if $section.af_tag:
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48 --af-tag '${section.af_tag}'
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49 #end if
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50 #if len($input_vcfs) == 1:
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51 ${section.split_by_ID}
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52 #end if
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53 ${section.verbose}
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54
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55 ## Stats section
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56 #set $section = $sec_restrict
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57 @APPLY_FILTERS@
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58 @COLLAPSE@
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59 @REGIONS@
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60 @SAMPLES@
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61 @TARGETS@
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62 @INCLUDE@
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63 @EXCLUDE@
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64
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65 ## Primary Input/Outputs
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66 @INPUT_FILES@
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67 > '$output_file'
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68 #if $plot_title:
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69 && plot-vcfstats
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70 -p 'plot_tmp/'
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71 -T '$plot_title'
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72 -s
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73 '$output_file'
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74 || (printf "The content of plot_tmp/plot-vcfstats.log is:\n" >&2 && cat plot_tmp/plot-vcfstats.log >&2 && exit 1)
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75 #end if
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76 ]]></command>
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77 <inputs>
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78 <expand macro="macro_input" />
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79 <param name="inputB_file" type="data" format="vcf,vcf_bgzip,bcf" optional="true" label="Optional VCF/BCF Data to compare against" help="When this second dataset is also specified, separate stats for intersection and the complements are generated" />
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80 <section name="sec_restrict" expanded="false" title="Restrict to">
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81 <expand macro="macro_samples" />
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82 <expand macro="macro_apply_filters" />
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83 <expand macro="macro_collapse" />
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84 <expand macro="macro_regions" />
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85 <expand macro="macro_targets" />
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86 <expand macro="macro_include" />
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87 <expand macro="macro_exclude" />
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88 </section>
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89 <section name="sec_default" expanded="true" title="Stats Options">
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90 <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="1St Allele Only"
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91 help="Include only 1st allele at multiallelic sites" />
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92 <conditional name="depth">
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93 <param name="set_depth" type="select" label="depth distribution: min,max,bin_size [0,500,1]">
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94 <option value="no">use depth defaults</option>
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95 <option value="yes">set depth</option>
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96 </param>
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97 <when value="no"/>
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98 <when value="yes">
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99 <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/>
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100 <param name="depth_max" type="integer" value="500" min="1" label="Depth max" />
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101 <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" />
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102 </when>
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103 </conditional>
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104 <expand macro="macro_fasta_ref" />
0
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105 <expand macro="macro_exons_file" />
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106 <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)"
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107 help="Collect stats for sites with ID separately (known vs novel)" />
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108 <param name="user_tstv" type="text" value="" optional="true" label="User Tstv"
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109 help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" >
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110 <validator type="regex" message="TAG optionally followed by :min:max:binsize">^([^ \t\n\r\f\v:,](:\d+:\d+:\d+)?)?$</validator>
5
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111 </param>
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112 <conditional name="afbins">
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113 <param name="afbins_select" type="select" label="Set af-bins">
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114 <option value="default">use default</option>
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115 <option value="af_bins_list">enter bins</option>
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116 <option value="af_bins_file">read bins from file</option>
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117 </param>
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118 <when value="default"/>
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119 <when value="af_bins_list">
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120 <param name="af_bins_list" type="text" value="0.1,0.5,1" label="list of allele frequency bins (e.g. 0.1,0.5,1)">
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121 <validator type="regex" message="comma-separated list of floats of increasing value">^[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?(,[-+]?(\d+(\.\d*)?|\.\d+)([eE][-+]?\d+)?)*$</validator>
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122 </param>
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123 </when>
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124 <when value="af_bins_file">
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125 <param name="af_bins_file" type="data" format="tabular" label="file listing the allele frequency bins one per line"/>
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126 </when>
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127 </conditional>
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128 <param name="af_tag" type="text" value="" optional="true" label="allele frequency tag to use, by default estimated from AN,AC or GT">
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129 <validator type="regex" message="TAG">^\w*$</validator>
0
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130 </param>
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131 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Verbose"
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132 help="Produce verbose per-site and per-sample output" />
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133 </section>
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134 <param name="plot_title" type="text" value="" optional="true" label="Create a plots pdf with this title">
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135 <validator type="regex" message="">^\w.*\w$</validator>
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136 </param>
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137 </inputs>
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138 <outputs>
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139 <data name="output_file" format="txt"/>
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140 <data name="output_pdf" format="pdf" from_work_dir="plot_tmp/summary.pdf">
0
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141 <filter>plot_title</filter>
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142 </data>
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143 </outputs>
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144 <tests>
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145 <test>
8
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146 <param name="input_file" ftype="vcf" value="stats.b.vcf" />
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147 <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
0
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148 <output name="output_file">
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149 <assert_contents>
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150 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
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151 <has_text_matching expression="SN\t1\tnumber of samples:\t3"/>
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152 </assert_contents>
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153 </output>
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154 </test>
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155 <test>
8
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156 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
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157 <param name="plot_title" value="Plot for mpileup.vcf" />
0
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158 <output name="output_file">
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159 <assert_contents>
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160 <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
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161 <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
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162 <has_text_matching expression="ST\t0\tA>C\t16"/>
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163 </assert_contents>
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164 </output>
8
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165 <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="20000" />
0
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166 </test>
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167 </tests>
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168 <help><![CDATA[
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169 =====================================
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170 bcftools @EXECUTABLE@
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171 =====================================
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172
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173 Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats.
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174
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175 When two files are given, the program generates separate stats for intersection and the complements.
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176 By default only sites are compared, -s/-S must given to include also sample columns.
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177
8
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178 When one VCF file is specified, then stats by non-reference allele frequency, depth distribution, stats by quality and per-sample counts, singleton stats, etc. are printed. When two VCF files are given, then stats such as concordance (Genotype concordance by non-reference allele frequency, Genotype concordance by sample, Non-Reference Discordance) and correlation are also printed. Per-site discordance (PSD) is also printed in --verbose mode.
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179
0
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180 @COLLAPSE_HELP@
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181 @REGIONS_HELP@
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182 @TARGETS_HELP@
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183 @EXPRESSIONS_HELP@
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184
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185 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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186
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187 @BCFTOOLS_WIKI@
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188 ]]>
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189 </help>
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190 <expand macro="citations" />
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191 </tool>