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1 <tool id="gatk_variant_combine" name="Combine Variants" version="0.0.4">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.4">gatk</requirement>
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5 </requirements>
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6 <macros>
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7 <import>gatk_macros.xml</import>
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8 </macros>
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9 <command interpreter="python">gatk_wrapper.py
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10 --max_jvm_heap_fraction "1"
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11 --stdout "${output_log}"
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12
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13 #set $priority_order = []
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14 #for $input_variant in $reference_source.input_variants:
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15 -d "--variant:${input_variant.input_variant_name},%(file_type)s" "${input_variant.input_variant}" "${input_variant.input_variant.ext}" "input_variant_${input_variant.input_variant_name}"
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16 #set $input_variant_name = str( $input_variant.input_variant_name )
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17 #assert $input_variant_name not in $priority_order, "Variant Names must be unique" ##this should be handled by a validator
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18 #silent $priority_order.append( $input_variant_name )
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19 #end for
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20 -p 'java
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21 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
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22 -T "CombineVariants"
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23 --out "${output_variants}"
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24 ##--num_threads 4 ##hard coded, for now
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25 -et "NO_ET" ##ET no phone home
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26 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
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27 #if $reference_source.reference_source_selector != "history":
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28 -R "${reference_source.ref_file.fields.path}"
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29 #end if
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30 --genotypemergeoption "${genotype_merge_option}"
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31 --rod_priority_list "${ ','.join( $priority_order ) }"
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32 '
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33
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34 #include source=$standard_gatk_options#
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35
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36
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37 ##start analysis specific options
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38 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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39 -p '
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40 --filteredrecordsmergetype "${analysis_param_type.filtered_records_merge_type}"
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41 ${analysis_param_type.print_complex_merges}
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42 ${analysis_param_type.filtered_are_uncalled}
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43 ${analysis_param_type.minimal_vcf}
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44 ${analysis_param_type.assume_identical_samples}
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45
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46 #if str( $analysis_param_type.set_key ):
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47 --setKey "${analysis_param_type.set_key}"
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48 #end if
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49
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50 --minimumN "${analysis_param_type.minimum_n}"
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51 '
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52 #end if
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53 </command>
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54 <inputs>
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55
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56 <conditional name="reference_source">
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57 <expand macro="reference_source_selector_param" />
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58 <when value="cached">
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59 <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &lt;variant&gt;)">
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60 <param name="input_variant" type="data" format="vcf" label="Input variant file" />
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61 <param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique">
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62 <validator type="length" min="1" message="You must provide a unique name for this set of variants" />
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63 </param>
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64 </repeat>
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65 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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66 <options from_data_table="gatk_picard_indexes">
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67 <!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> -->
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68 </options>
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69 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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70 </param>
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71 </when>
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72 <when value="history"> <!-- FIX ME!!!! -->
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73 <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &lt;variant&gt;)">
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74 <param name="input_variant" type="data" format="vcf" label="Input variant file" />
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75 <param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique">
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76 <validator type="length" min="1" message="You must provide a unique name for this set of variants" />
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77 </param>
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78 </repeat>
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79 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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80 </when>
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81 </conditional>
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82
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83 <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" help="-genotypeMergeOptions,--genotypemergeoption &lt;genotypemergeoption&gt;" >
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84 <option value="UNIQUIFY" />
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85 <option value="PRIORITIZE" selected="true"/>
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86 <option value="UNSORTED" />
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87 <option value="REQUIRE_UNIQUE" />
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88 </param>
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89
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90 <expand macro="gatk_param_type_conditional" />
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91
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92
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93 <expand macro="analysis_type_conditional">
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94 <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype &lt;filteredrecordsmergetype&gt;" >
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95 <option value="KEEP_IF_ANY_UNFILTERED" selected="true"/>
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96 <option value="KEEP_IF_ALL_UNFILTERED" />
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97 </param>
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98
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99 <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,--printComplexMerges" />
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100 <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" help="-filteredAreUncalled,--filteredAreUncalled" />
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101 <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" help="-minimalVCF,--minimalVCF" />
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102
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103 <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from." help="-setKey,--setKey &lt;setKey&gt;"/>
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104 <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" />
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105 <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN &lt;minimumN&gt;"/>
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106
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107 </expand>
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108
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109
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110 </inputs>
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111 <outputs>
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112 <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (variants)" />
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113 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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114 </outputs>
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115 <tests>
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116 <test>
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117 <param name="reference_source_selector" value="history" />
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118 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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119 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
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120 <param name="input_variant_name" value="from_variant_annotator" />
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121 <param name="genotype_merge_option" value="PRIORITIZE" />
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122 <param name="gatk_param_type_selector" value="basic" />
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123 <param name="analysis_param_type_selector" value="basic" />
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124 <output name="output_variants" file="gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf" lines_diff="4" />
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125 <output name="output_log" file="gatk/gatk_variant_combine/gatk_variant_combine_out_1.log.contains" compare="contains" />
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126 </test>
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127 </tests>
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128 <help>
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129 **What it does**
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130
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131 Combines VCF records from different sources; supports both full merges and set unions. Merge: combines multiple records into a single one; if sample names overlap then they are uniquified. Union: assumes each rod represents the same set of samples (although this is not enforced); using the priority list (if provided), emits a single record instance at every position represented in the rods.
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132
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133 For more information on using the CombineVariants module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/CombineVariants>`_.
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134
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135 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_.
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136
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137 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_.
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138
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139 ------
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140
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141 **Inputs**
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142
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143 GenomeAnalysisTK: CombineVariants accepts variant files as input.
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144
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145 ------
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146
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147 **Outputs**
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148
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149 The output is a combined vcf file.
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150
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151
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152 Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats.
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153
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154 -------
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155
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156 **Settings**::
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157
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158 out File to which variants should be written
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159 genotypemergeoption How should we merge genotype records for samples shared across the ROD files? (UNIQUIFY|PRIORITIZE|UNSORTED|REQUIRE_UNIQUE)
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160 filteredrecordsmergetype How should we deal with records seen at the same site in the VCF, but with different FILTER fields? KEEP_IF_ANY_UNFILTERED PASSes the record if any record is unfiltered, KEEP_IF_ALL_UNFILTERED requires all records to be unfiltered (KEEP_IF_ANY_UNFILTERED|KEEP_IF_ALL_UNFILTERED)
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161 rod_priority_list When taking the union of variants containing genotypes: a comma-separated string describing the priority ordering for the genotypes as far as which record gets emitted; a complete priority list MUST be provided
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162 printComplexMerges Print out interesting sites requiring complex compatibility merging
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163 filteredAreUncalled If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF
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164 minimalVCF If true, then the output VCF will contain no INFO or genotype INFO field
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165 setKey Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from. Set to null if you don't want the set field emitted.
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166 assumeIdenticalSamples If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime.
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167 minimumN Combine variants and output site only if variant is present in at least N input files.
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168
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169 @CITATION_SECTION@
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170 </help>
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171 </tool>
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