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1 <tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.1">
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2 <description></description>
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3 <macros>
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4 <import>gatk2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command interpreter="python">
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9 gatk2_wrapper.py
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10 --stdout "${output_log}"
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11 #for $var_count, $variant in enumerate( $reference_source.input_variants ):
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12 -d "--input:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}"
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13 #end for
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14 -p '
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15 @JAR_PATH@
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16 -T "ApplyRecalibration"
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17 \$GATK2_SITE_OPTIONS
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18
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19 @THREADS@
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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 --recal_file "${reference_source.input_recal}"
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25 --tranches_file "${reference_source.input_tranches}"
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26 --out "${output_variants}"
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27 '
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28
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29 #include source=$standard_gatk_options#
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30
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31 ##start analysis specific options
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32 -p '
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33 --mode "${mode}"
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34
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35 #for $ignore_filter in $ignore_filters:
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36 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
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37 #if $ignore_filter_name == "custom":
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38 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
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39 #end if
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40 --ignore_filter "${ignore_filter_name}"
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41 #end for
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42 --ts_filter_level "${ts_filter_level}"
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43 '
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44 </command>
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45 <inputs>
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46 <conditional name="reference_source">
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47 <expand macro="reference_source_selector_param" />
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48 <when value="cached">
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49 <expand macro="input_variants" />
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50 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" />
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51 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" />
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52 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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53 <options from_data_table="gatk2_picard_indexes">
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54 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
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55 </options>
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56 <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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57 </param>
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58 </when>
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59 <when value="history"> <!-- FIX ME!!!! -->
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60 <expand macro="input_variants" />
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61 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" />
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62 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" />
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63 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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64 </when>
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65 </conditional>
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66
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67 <expand macro="gatk_param_type_conditional" />
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68
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69 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &lt;mode&gt;">
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70 <option value="SNP" selected="True">SNP</option>
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71 <option value="INDEL">INDEL</option>
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72 <option value="BOTH">BOTH</option>
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73 </param>
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74 <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &lt;ignore_filter&gt;">
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75 <conditional name="ignore_filter_type">
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76 <param name="ignore_filter_type_selector" type="select" label="Filter Type">
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77 <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option>
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78 <option value="LowQual" >LowQual</option>
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79 <option value="custom" selected="True">Other</option>
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80 </param>
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81 <when value="custom">
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82 <param name="filter_name" type="text" value="" label="Filter name"/>
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83 </when>
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84 <when value="HARD_TO_VALIDATE" />
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85 <when value="LowQual" />
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86 </conditional>
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87 </repeat>
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88 <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &lt;ts_filter_level&gt;"/>
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89 </inputs>
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90 <outputs>
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91 <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (Variants File)" />
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92 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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93 </outputs>
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94 <tests>
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95 <!-- ADD TESTS -->
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96 </tests>
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97 <help>
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98 **What it does**
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99
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100 Applies cuts to the input vcf file (by adding filter lines) to achieve the desired novel FDR levels which were specified during VariantRecalibration
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101
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102 For more information on using the ApplyRecalibration module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantrecalibration_ApplyRecalibration.html>`_.
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103
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104 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_.
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105
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106 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.
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107
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108 ------
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109
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110 **Inputs**
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111
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112 GenomeAnalysisTK: ApplyRecalibration accepts a variant input file, a recalibration file and a tranches file.
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113
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114
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115 **Outputs**
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116
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117 The output is in VCF format.
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118
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119 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats.
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120
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121 -------
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122
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123 **Settings**::
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124
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125
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126 recal_file The output recal file used by ApplyRecalibration
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127 tranches_file The input tranches file describing where to cut the data
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128 out The output filtered, recalibrated VCF file
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129 ts_filter_level The truth sensitivity level at which to start filtering
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130 ignore_filter If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file
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131 mode Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously. (SNP|INDEL|BOTH)
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132
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133 @CITATION_SECTION@
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134 </help>
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135 <expand macro="citations" />
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136 </tool>
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