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1 <tool id="gatk_variant_select" name="Select Variants" version="0.0.2">
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2 <description>from VCF files</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 #from binascii import hexlify
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11 --max_jvm_heap_fraction "1"
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12 --stdout "${output_log}"
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13 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
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14 -p 'java
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15 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
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16 -T "SelectVariants"
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17 --num_threads \${GALAXY_SLOTS:-4}
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18 -et "NO_ET" ##ET no phone home
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19 -o "${output_vcf}"
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20
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21 #if $reference_source.reference_source_selector != "history":
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22 -R "${reference_source.ref_file.fields.path}"
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23 #end if
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24 '
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25 -p '
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26 #if $input_concordance:
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27 --concordance "${input_concordance}"
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28 #end if
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29 #if $input_discordance:
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30 --discordance "${input_discordance}"
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31 #end if
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32
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33 #for $exclude_sample_name in $exclude_sample_name_repeat:
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34 --exclude_sample_name "${exclude_sample_name.exclude_sample_name}"
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35 #end for
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36
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37 ${exclude_filtered}
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38
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39 #for $sample_name in $sample_name_repeat:
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40 --sample_name "${sample_name.sample_name}"
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41 #end for
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42
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43 '
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44
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45 #for $select_expressions in $select_expressions_repeat:
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46 #set $select_expression = "--select_expressions '%s'" % ( str( $select_expressions.select_expressions ) )
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47 -o '${ hexlify( $select_expression ) }'
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48 #end for
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49
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50 ##start tool specific options
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51 #if str( $analysis_param_type.analysis_param_type_selector ) == 'advanced':
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52 -p '
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53 #for $exclude_sample_file in $analysis_param_type.exclude_sample_file_repeat:
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54 --exclude_sample_file "${exclude_sample_file.exclude_sample_file}"
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55 #end for
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56
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57 #for $sample_file in $analysis_param_type.sample_file_repeat:
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58 --sample_file "${ample_file.sample_file}"
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59 #end for
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60
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61 #if $analysis_param_type.input_keep_ids:
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62 --keepIDs "${analysis_param_type.input_keep_ids}"
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63 #end if
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64
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65 ${analysis_param_type.keep_original_AC}
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66
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67 ${analysis_param_type.mendelian_violation}
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68
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69 --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}"
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70
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71 --remove_fraction_genotypes "${analysis_param_type.remove_fraction_genotypes}"
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72
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73 --restrictAllelesTo "${analysis_param_type.restrict_alleles_to}"
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74
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75 #if str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_fraction':
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76 --select_random_fraction "${analysis_param_type.select_random_type.select_random_fraction}"
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77 #elif str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_number':
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78 --select_random_number "${analysis_param_type.select_random_type.select_random_number}"
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79 #end if
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80
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81 #if $analysis_param_type.select_type_to_include:
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82 #for $type_to_include in str( $analysis_param_type.select_type_to_include ).split( ',' ):
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83 --selectTypeToInclude "${type_to_include}"
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84 #end for
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85 #end if
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86
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87 ${analysis_param_type.exclude_non_variants}
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88 '
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89
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90 #for $sample_expressions in $analysis_param_type.sample_expressions_repeat:
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91 #set $sample_expression = "--sample_expressions '%s'" % ( str( $sample_expressions.sample_expressions ) )
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92 -o '${ hexlify( $sample_expression ) }'
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93 #end for
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94
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95 #end if
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96 ##end tool specific options
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97
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98 #include source=$standard_gatk_options#
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99
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100
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101 </command>
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102 <inputs>
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103 <conditional name="reference_source">
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104 <expand macro="reference_source_selector_param" />
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105 <when value="cached">
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106 <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &lt;variant&gt;" />
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107 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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108 <options from_data_table="gatk_picard_indexes">
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109 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
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110 </options>
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111 <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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112 </param>
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113 </when>
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114 <when value="history"> <!-- FIX ME!!!! -->
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115 <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &lt;variant&gt;" />
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116 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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117 </when>
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118 </conditional>
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119
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120 <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data" help="-select,--select_expressions &lt;select_expressions&gt;">
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121 <param name="select_expressions" type="text" label="JEXL expression">
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122 <sanitizer>
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123 <valid initial="string.printable">
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124 <remove value="'"/>
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125 </valid>
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126 <mapping initial="none"/>
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127 </sanitizer>
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128 </param>
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129 </repeat>
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130
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131 <param name="input_concordance" type="data" format="vcf" label="Output variants that were also called in this comparison track" optional="True" help="-conc,--concordance &lt;concordance&gt;"/>
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132 <param name="input_discordance" type="data" format="vcf" label="Output variants that were not called in this comparison track" optional="True" help="-disc,--discordance &lt;discordance&gt;"/>
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133
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134 <repeat name="sample_name_repeat" title="Include Samples by name" help="-sn,--sample_name &lt;sample_name&gt;">
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135 <param name="sample_name" type="text" label="Include genotypes from this sample"/>
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136 </repeat>
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137
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138 <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name" help="-xl_sn,--exclude_sample_name &lt;exclude_sample_name&gt;">
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139 <param name="exclude_sample_name" type="text" label="Exclude genotypes from this sample"/>
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140 </repeat>
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141
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142 <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" help="-ef,--excludeFiltered" />
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143
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144 <expand macro="gatk_param_type_conditional" />
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145
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146
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147 <expand macro="analysis_type_conditional">
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148
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149 <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file &lt;exclude_sample_file&gt;">
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150 <param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/>
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151 </repeat>
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152
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153 <repeat name="sample_file_repeat" title="Samples by file" help="-sf,--sample_file &lt;sample_file&gt;">
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154 <param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" />
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155 </repeat>
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156
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157 <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &lt;keepIDs&gt;"/>
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158
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159 <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" help="-keepOriginalAC,--keepOriginalAC" />
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160
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161 <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" help="-mv,--mendelianViolation" />
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162
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163 <param name="mendelian_violation_qual_threshold" type="float" label="Minimum genotype QUAL score for each trio member required to accept a site as a mendelian violation" value="0" help="-mvq,--mendelianViolationQualThreshold &lt;mendelianViolationQualThreshold&gt;" />
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164
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165 <param name="remove_fraction_genotypes" type="float" label="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall" value="0" min="0" max="1" help="-fractionGenotypes,--remove_fraction_genotypes &lt;remove_fraction_genotypes&gt;" />
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166
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167 <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity" help="-restrictAllelesTo,--restrictAllelesTo &lt;restrictAllelesTo&gt;">
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168 <option value="ALL" selected="True">ALL</option>
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169 <option value="MULTIALLELIC">MULTIALLELIC</option>
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170 <option value="BIALLELIC">BIALLELIC</option>
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171 </param>
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172
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173 <repeat name="sample_expressions_repeat" title="Regular expression to select many samples from the ROD tracks provided" help="-se,--sample_expressions &lt;sample_expressions&gt;">
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174 <param name="sample_expressions" type="text" label="Regular expression">
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175 <sanitizer>
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176 <valid initial="string.printable">
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177 <remove value="'"/>
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178 </valid>
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179 <mapping initial="none"/>
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180 </sanitizer>
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181 </param>
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182 </repeat>
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183
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184 <conditional name="select_random_type">
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185 <param name="select_random_type_selector" type="select" label="Select a random subset of variants">
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186 <option value="select_all" selected="True">Use all variants</option>
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187 <option value="select_random_fraction">Select random fraction</option>
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188 <option value="select_random_number">Select random number</option>
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189 </param>
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190 <when value="select_all">
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191 <!-- Do nothing here -->
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192 </when>
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193 <when value="select_random_fraction">
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194 <param name="select_random_fraction" type="float" value="0" label="Fraction" min="0" max="1" help="-fraction,--select_random_fraction &lt;select_random_fraction&gt;"/>
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195 </when>
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196 <when value="select_random_number">
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197 <param name="select_random_number" type="integer" value="0" label="Count" help="-number,--select_random_number &lt;select_random_number&gt;" />
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198 </when>
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199 </conditional>
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200
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201 <param name="exclude_non_variants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the subsetting procedure" help="-env,--excludeNonVariants" />
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202
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203 <param name="select_type_to_include" type="select" label="Select only a certain type of variants from the input file" multiple="True" display="checkboxes" help="-selectType,--selectTypeToInclude &lt;selectTypeToInclude&gt;">
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204 <option value="INDEL">INDEL</option>
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205 <option value="SNP">SNP</option>
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206 <option value="MIXED">MIXED</option>
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207 <option value="MNP">MNP</option>
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208 <option value="SYMBOLIC">SYMBOLIC</option>
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209 <option value="NO_VARIATION">NO_VARIATION</option>
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210 </param>
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211 </expand>
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212
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213 </inputs>
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214 <outputs>
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215 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
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216 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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217 </outputs>
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218 <tests>
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219 <test>
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220 <param name="reference_source_selector" value="history" />
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221 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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222 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
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223 <param name="select_expressions_repeat" value="0" />
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224 <param name="input_concordance" />
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225 <param name="input_discordance" />
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226 <param name="exclude_sample_name_repeat" value="0" />
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227 <param name="exclude_filtered" />
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228 <param name="sample_name_repeat" value="0" />
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229 <param name="gatk_param_type_selector" value="basic" />
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230 <param name="analysis_param_type_selector" value="basic" />
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231 <output name="output_vcf" file="gatk/gatk_variant_select/gatk_variant_select_out_1.vcf" lines_diff="4" />
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232 <output name="output_log" file="gatk/gatk_variant_select/gatk_variant_select_out_1.log.contains" compare="contains" />
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233 </test>
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234 </tests>
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235 <help>
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236 **What it does**
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237
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238 Often, a VCF containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like IGV, etc.). SelectVariants can be used for this purpose. Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion, i.e. "DP > 1000" (depth of coverage greater than 1000x), "AF < 0.25" (sites with allele frequency less than 0.25). These JEXL expressions are documented in the Using JEXL expressions section (http://www.broadinstitute.org/gsa/wiki/index.php/Using_JEXL_expressions). One can optionally include concordance or discordance tracks for use in selecting overlapping variants.
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239
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240 For more information on using the SelectVariants module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/SelectVariants>`_.
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241
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242 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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243
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244 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_.
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245
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246 ------
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247
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248 **Inputs**
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249
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250 GenomeAnalysisTK: SelectVariants accepts a VCF input file.
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251
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252
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253 **Outputs**
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254
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255 The output is in VCF format.
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256
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257
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258 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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259
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260 -------
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261
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262 **Settings**::
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263
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264
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265 out VCFWriter stdout File to which variants should be written
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266 variant RodBinding[VariantContext] NA Input VCF file
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267 concordance RodBinding[VariantContext] none Output variants that were also called in this comparison track
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268 discordance RodBinding[VariantContext] none Output variants that were not called in this comparison track
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269 exclude_sample_file Set[File] [] File containing a list of samples (one per line) to exclude. Can be specified multiple times
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270 exclude_sample_name Set[String] [] Exclude genotypes from this sample. Can be specified multiple times
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271 excludeFiltered boolean false Don't include filtered loci in the analysis
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272 excludeNonVariants boolean false Don't include loci found to be non-variant after the subsetting procedure
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273 keepIDs File NA Only emit sites whose ID is found in this file (one ID per line)
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274 keepOriginalAC boolean false Don't update the AC, AF, or AN values in the INFO field after selecting
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275 mendelianViolation Boolean false output mendelian violation sites only
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276 mvq double 0.0 Minimum genotype QUAL score for each trio member required to accept a site as a violation
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277 remove_fraction_genotypes double 0.0 Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall
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278 restrictAllelesTo NumberAlleleRestriction ALL Select only variants of a particular allelicity. Valid options are ALL (default), MULTIALLELIC or BIALLELIC
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279 sample_expressions Set[String] NA Regular expression to select many samples from the ROD tracks provided. Can be specified multiple times
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280 sample_file Set[File] NA File containing a list of samples (one per line) to include. Can be specified multiple times
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281 sample_name Set[String] [] Include genotypes from this sample. Can be specified multiple times
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282 select_expressions ArrayList[String] [] One or more criteria to use when selecting the data
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283 select_random_fraction double 0.0 Selects a fraction (a number between 0 and 1) of the total variants at random from the variant track
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284 select_random_number int 0 Selects a number of variants at random from the variant track
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285 selectTypeToInclude List[Type] [] Select only a certain type of variants from the input file. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Can be specified multiple times
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286
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287 @CITATION_SECTION@
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288 </help>
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289 </tool>
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