annotate variant_annotator.xml @ 34:b99c25b0ad4d draft

Update tool version to 0.0.7
author Jim Johnson <jj@umn.edu>
date Thu, 28 Feb 2013 15:41:24 -0600
parents 76f8ca47b810
children a29c7d7d962d
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1 <tool id="gatk2_variant_annotator" name="Variant Annotator" version="0.0.7">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="2.3">gatk</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 </requirements>
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7 <command interpreter="python">gatk2_wrapper.py
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8 --max_jvm_heap_fraction "1"
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9 --stdout "${output_log}"
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10 #if str( $reference_source.input_bam ) != "None":
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11 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
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12 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
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13 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
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14 #end if
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15 #end if
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16 -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
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17 -p 'java
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18 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
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19 ##--list
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20 -T "VariantAnnotator"
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21 \$GATK2_SITE_OPTIONS
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22 ## \$GATK2_NUM_THREADS
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23 ##--num_threads 4 ##hard coded, for now
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24 ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
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25 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
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26 #if $reference_source.reference_source_selector != "history":
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27 -R "${reference_source.ref_file.fields.path}"
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28 #end if
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29 -o "${output_vcf}"
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30 #if str( $annotations_type.annotations_type_selector ) == "use_all_annotations":
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31 --useAllAnnotations
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32 #else:
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33 #if $annotations_type.annotations:
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34 #for $annotation in str( $annotations_type.annotations.fields.gatk_value ).split( ',' ):
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35 --annotation "${annotation}"
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36 #end for
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37 #end if
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38 #end if
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39 #if $exclude_annotations:
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40 #for $annotation in str( $exclude_annotations.fields.gatk_value ).split( ',' ):
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41 --excludeAnnotation "${annotation}"
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42 #end for
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43 #end if
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44 #for $additional_annotation in $additional_annotations:
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45 --annotation "${additional_annotation.additional_annotation_name}"
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46 #end for
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47 '
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48 #if $reference_source.input_variant_bti:
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49 -d "--intervals" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant_bti"
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50 #end if
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51
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52 #for $rod_binding in $comp_rod_bind:
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53 -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
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54 #end for
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55
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56 #if str( $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector ) == 'set_dbsnp':
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57 -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
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58 #end if
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59
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60
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61 #for $rod_binding in $resource_rod_bind:
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62 -d "--resource:${rod_binding.resource_rod_name},%(file_type)s" "${rod_binding.resource_input_rod}" "${rod_binding.resource_input_rod.ext}" "input_resource_${rod_binding.resource_rod_name}"
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63 #end for
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64
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65 #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
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66 -p '--annotation "SnpEff"'
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67 -d "--snpEffFile:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}"
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68 #else:
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69 -p '--excludeAnnotation "SnpEff"'
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70 #end if
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71
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72 #for $expression in $expressions:
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73 -p '--expression "${expression.expression}"'
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74 #end for
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75
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76 ##start standard gatk options
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77 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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78 #for $pedigree in $gatk_param_type.pedigree:
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79 -p '--pedigree "${pedigree.pedigree_file}"'
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80 #end for
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81 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
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82 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
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83 #end for
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84 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
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85 #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
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86 #for $read_filter in $gatk_param_type.read_filter:
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87 -p '
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88 #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters:
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89 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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90 #end_if
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91 #for $name, $param in $read_filter.read_filter_type.iteritems():
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92 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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93 #if hasattr( $param.input, 'truevalue' ):
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94 ${param}
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95 #else:
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96 --${name} "${param}"
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97 #end if
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98 #end if
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99 #end for
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100 '
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101 #end for
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102 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
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103 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
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104 #end for
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105
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106 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
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107 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
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108 #end for
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109
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110 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
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111
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112 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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113 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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114 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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115 #end if
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116 -p '
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117 --baq "${gatk_param_type.baq}"
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118 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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119 ${gatk_param_type.use_original_qualities}
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120 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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121 --validation_strictness "${gatk_param_type.validation_strictness}"
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122 --interval_merging "${gatk_param_type.interval_merging}"
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123 ${gatk_param_type.disable_experimental_low_memory_sharding}
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124 ${gatk_param_type.fix_misencoded_quality_scores}
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125 ${gatk_param_type.non_deterministic_random_seed}
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126 '
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127 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
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128 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
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129 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
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130 #else
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131 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
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132 #end if
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133 #end for
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134 #end if
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135 #if str( $reference_source.reference_source_selector ) == "history":
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136 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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137 #end if
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138 ##end standard gatk options
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139
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140 -p '
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141 #if str( $annotation_group ) != "None":
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142 #for $group in str( $annotation_group ).split( ',' ):
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143 --group "${group}"
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144 #end for
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145 #end if
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146 #if str( $family_string ) != "":
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147 --family_string "${family_string}"
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148 #end if
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149 --MendelViolationGenotypeQualityThreshold "${mendel_violation_genotype_quality_threshold}"
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150 '
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151 </command>
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152 <inputs>
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153 <conditional name="reference_source">
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154 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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155 <option value="cached">Locally cached</option>
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156 <option value="history">History</option>
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157 </param>
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158 <when value="cached">
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159 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
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160 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/>
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161 <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" >
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162 <validator type="unspecified_build" />
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163 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
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164 </param>
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165 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
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166 <options from_data_table="gatk2_picard_indexes">
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167 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
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168 </options>
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169 <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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170 </param>
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171 </when>
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172 <when value="history"> <!-- FIX ME!!!! -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
173 <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
174 <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
175 <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
176 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
177 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
178 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
179 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
180 <conditional name="annotations_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
181 <param name="annotations_type_selector" type="select" label="Use all possible annotations">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
182 <option value="use_all_annotations">Use all</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
183 <option value="choose" selected="True">Use selected</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
184 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
185 <when value="use_all_annotations">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
186 <!-- no extra options here -->
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jjohnson
parents:
diff changeset
187 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
188 <when value="choose">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
189 <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" help="-A,--annotation &amp;lt;annotation&amp;gt;" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
190 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
191 <options from_data_table="gatk2_annotations">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
192 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
193 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
194 </options>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
195 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
196 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
197 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
198
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
199 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
200 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
201 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
202
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
203 <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp &amp;lt;comp&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
204 <param name="comp_input_rod" type="data" format="vcf" label="ROD file" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
205 <param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
206 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
207
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
208 <conditional name="dbsnp_rod_bind_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
209 <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
210 <option value="set_dbsnp" selected="True">Set dbSNP</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
211 <option value="exclude_dbsnp">Don't set dbSNP</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
212 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
213 <when value="exclude_dbsnp">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
214 <!-- Do nothing here -->
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jjohnson
parents:
diff changeset
215 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
216 <when value="set_dbsnp">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
217 <param name="dbsnp_input_rod" type="data" format="vcf" label="ROD file" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
218 <param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="ROD Name"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
219 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
220 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
221
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
222 <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource &amp;lt;resource&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
223 <param name="resource_input_rod" type="data" format="vcf" label="ROD file" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
224 <param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
225 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
226
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
227 <conditional name="snpEff_rod_bind_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
228 <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file" help="-snpEffFile,--snpEffFile &amp;lt;snpEffFile&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
229 <option value="set_snpEff">Set snpEff</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
230 <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
231 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
232 <when value="exclude_snpEff">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
233 <!-- Do nothing here -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
234 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
235 <when value="set_snpEff">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
236 <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
237 <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
238 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
239 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
240
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
241 <repeat name="expressions" title="Expression" help="-E,--expression &amp;lt;expression&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
242 <param name="expression" type="text" value="" label="Expression"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
243 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
244
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
245 <conditional name="gatk_param_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
246 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
247 <option value="basic" selected="True">Basic</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
248 <option value="advanced">Advanced</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
249 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
250 <when value="basic">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
251 <!-- Do nothing here -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
252 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
253 <when value="advanced">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
254 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
255 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
256 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
257 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
258 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
259 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
260 <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
261 <option value="STRICT" selected="True">STRICT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
262 <option value="SILENT">SILENT</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
263 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
264 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
265 <conditional name="read_filter_type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
266 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
267 <option value="BadCigar">BadCigar</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
268 <option value="BadMate">BadMate</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
269 <option value="DuplicateRead">DuplicateRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
270 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
271 <option value="MalformedRead">MalformedRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
272 <option value="MappingQuality">MappingQuality</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
273 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
274 <option value="MappingQualityZero">MappingQualityZero</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
275 <option value="MateSameStrand">MateSameStrand</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
276 <option value="MaxInsertSize">MaxInsertSize</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
277 <option value="MaxReadLength" selected="True">MaxReadLength</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
278 <option value="MissingReadGroup">MissingReadGroup</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
279 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
280 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
281 <option value="Platform454">Platform454</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
282 <option value="Platform">Platform</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
283 <option value="PlatformUnit">PlatformUnit</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
284 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
285 <option value="ReadName">ReadName</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
286 <option value="ReadStrand">ReadStrand</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
287 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
288 <option value="Sample">Sample</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
289 <option value="SingleReadGroup">SingleReadGroup</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
290 <option value="UnmappedRead">UnmappedRead</option>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
291 </param>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
292 <when value="BadCigar">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
293 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
294 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
295 <when value="BadMate">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
296 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
297 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
298 <when value="DuplicateRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
299 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
300 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
301 <when value="FailsVendorQualityCheck">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
302 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
303 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
304 <when value="MalformedRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
305 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
306 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
307 <when value="MappingQuality">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
308 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
309 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
310 <when value="MappingQualityUnavailable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
311 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
312 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
313 <when value="MappingQualityZero">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
314 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
315 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
316 <when value="MateSameStrand">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
317 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
318 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
319 <when value="MaxInsertSize">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
320 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
321 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
322 <when value="MaxReadLength">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
323 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
324 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
325 <when value="MissingReadGroup">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
326 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
327 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
328 <when value="NoOriginalQualityScores">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
329 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
330 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
331 <when value="NotPrimaryAlignment">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
332 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
333 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
334 <when value="Platform454">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
335 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
336 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
337 <when value="Platform">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
338 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
339 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
340 <when value="PlatformUnit">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
341 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
342 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
343 <when value="ReadGroupBlackList">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
344 <!-- no extra options -->
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
345 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
346 <when value="ReadName">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
347 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
348 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
349 <when value="ReadStrand">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
350 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
351 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
352 <when value="ReassignMappingQuality">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
353 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
354 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
355 <when value="Sample">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
356 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
357 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
358 <when value="SingleReadGroup">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
359 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
360 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
361 <when value="UnmappedRead">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
362 <!-- no extra options -->
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jjohnson
parents:
diff changeset
363 </when>
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jjohnson
parents:
diff changeset
364 </conditional>
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jjohnson
parents:
diff changeset
365 </repeat>
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jjohnson
parents:
diff changeset
366 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
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jjohnson
parents:
diff changeset
367 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
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jjohnson
parents:
diff changeset
368 </repeat>
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jjohnson
parents:
diff changeset
369 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
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jjohnson
parents:
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370 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
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jjohnson
parents:
diff changeset
371 </repeat>
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jjohnson
parents:
diff changeset
372
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jjohnson
parents:
diff changeset
373 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
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jjohnson
parents:
diff changeset
374 <option value="UNION" selected="True">UNION</option>
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jjohnson
parents:
diff changeset
375 <option value="INTERSECTION">INTERSECTION</option>
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jjohnson
parents:
diff changeset
376 </param>
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jjohnson
parents:
diff changeset
377
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jjohnson
parents:
diff changeset
378 <conditional name="downsampling_type">
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jjohnson
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diff changeset
379 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
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jjohnson
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380 <option value="NONE" selected="True">NONE</option>
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jjohnson
parents:
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381 <option value="ALL_READS">ALL_READS</option>
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jjohnson
parents:
diff changeset
382 <option value="BY_SAMPLE">BY_SAMPLE</option>
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jjohnson
parents:
diff changeset
383 </param>
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jjohnson
parents:
diff changeset
384 <when value="NONE">
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jjohnson
parents:
diff changeset
385 <!-- no more options here -->
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jjohnson
parents:
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386 </when>
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jjohnson
parents:
diff changeset
387 <when value="ALL_READS">
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jjohnson
parents:
diff changeset
388 <conditional name="downsample_to_type">
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jjohnson
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389 <param name="downsample_to_type_selector" type="select" label="Downsample method">
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jjohnson
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390 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
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jjohnson
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diff changeset
391 <option value="downsample_to_coverage">Downsample by Coverage</option>
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jjohnson
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diff changeset
392 </param>
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jjohnson
parents:
diff changeset
393 <when value="downsample_to_fraction">
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jjohnson
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394 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
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jjohnson
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diff changeset
395 </when>
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jjohnson
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396 <when value="downsample_to_coverage">
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jjohnson
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397 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
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jjohnson
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398 </when>
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jjohnson
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399 </conditional>
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jjohnson
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400 </when>
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jjohnson
parents:
diff changeset
401 <when value="BY_SAMPLE">
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jjohnson
parents:
diff changeset
402 <conditional name="downsample_to_type">
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jjohnson
parents:
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403 <param name="downsample_to_type_selector" type="select" label="Downsample method">
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jjohnson
parents:
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404 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
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jjohnson
parents:
diff changeset
405 <option value="downsample_to_coverage">Downsample by Coverage</option>
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jjohnson
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diff changeset
406 </param>
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jjohnson
parents:
diff changeset
407 <when value="downsample_to_fraction">
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jjohnson
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408 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
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jjohnson
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diff changeset
409 </when>
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jjohnson
parents:
diff changeset
410 <when value="downsample_to_coverage">
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jjohnson
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411 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
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jjohnson
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412 </when>
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jjohnson
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413 </conditional>
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jjohnson
parents:
diff changeset
414 </when>
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jjohnson
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415 </conditional>
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jjohnson
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diff changeset
416 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
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jjohnson
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417 <option value="OFF" selected="True">OFF</option>
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jjohnson
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diff changeset
418 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
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jjohnson
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diff changeset
419 <option value="RECALCULATE">RECALCULATE</option>
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jjohnson
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diff changeset
420 </param>
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jjohnson
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421 <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
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jjohnson
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422 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
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jjohnson
parents:
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423 <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
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jjohnson
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424 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
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jjohnson
parents:
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425 <option value="STRICT" selected="True">STRICT</option>
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jjohnson
parents:
diff changeset
426 <option value="LENIENT">LENIENT</option>
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jjohnson
parents:
diff changeset
427 <option value="SILENT">SILENT</option>
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jjohnson
parents:
diff changeset
428 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
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jjohnson
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429 </param>
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jjohnson
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diff changeset
430 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
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jjohnson
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431 <option value="ALL" selected="True">ALL</option>
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jjohnson
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diff changeset
432 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
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jjohnson
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diff changeset
433 </param>
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jjohnson
parents:
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434
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jjohnson
parents:
diff changeset
435 <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
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jjohnson
parents:
diff changeset
436 <conditional name="read_group_black_list_type">
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jjohnson
parents:
diff changeset
437 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
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jjohnson
parents:
diff changeset
438 <option value="file" selected="True">Filters in file</option>
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jjohnson
parents:
diff changeset
439 <option value="text">Specify filters as a string</option>
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jjohnson
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diff changeset
440 </param>
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jjohnson
parents:
diff changeset
441 <when value="file">
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jjohnson
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diff changeset
442 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
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jjohnson
parents:
diff changeset
443 </when>
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jjohnson
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diff changeset
444 <when value="text">
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jjohnson
parents:
diff changeset
445 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
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jjohnson
parents:
diff changeset
446 </when>
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jjohnson
parents:
diff changeset
447 </conditional>
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jjohnson
parents:
diff changeset
448 </repeat>
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jjohnson
parents:
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449
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jjohnson
parents:
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450 <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
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jjohnson
parents:
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451 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
18
7533db8dfb5b Update tool_dependencies to GATK v 2.3
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
452 <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False" help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
0
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jjohnson
parents:
diff changeset
453
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jjohnson
parents:
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454 </when>
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jjohnson
parents:
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455 </conditional>
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jjohnson
parents:
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456
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jjohnson
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457 <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls" help="-G,--group &amp;lt;group&amp;gt;">
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jjohnson
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diff changeset
458 <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
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jjohnson
parents:
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459 <option value="Standard">Standard</option>
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jjohnson
parents:
diff changeset
460 <option value="Experimental">Experimental</option>
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jjohnson
parents:
diff changeset
461 <option value="WorkInProgress">WorkInProgress</option>
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jjohnson
parents:
diff changeset
462 <option value="RankSumTest">RankSumTest</option>
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jjohnson
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diff changeset
463 </param>
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jjohnson
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diff changeset
464 <param name="family_string" type="text" value="" label="Family String" help="--family_string"/>
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jjohnson
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diff changeset
465 <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio." help="-mvq,--MendelViolationGenotypeQualityThreshold &amp;lt;MendelViolationGenotypeQualityThreshold&amp;gt;"/>
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jjohnson
parents:
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466 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
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jjohnson
parents:
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467 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
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jjohnson
parents:
diff changeset
468 <options from_data_table="gatk2_annotations">
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jjohnson
parents:
diff changeset
469 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
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jjohnson
parents:
diff changeset
470 <filter type="static_value" value="VariantAnnotator" column="tools_valid_for"/>
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jjohnson
parents:
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471 </options>
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jjohnson
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472 </param>
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jjohnson
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473
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jjohnson
parents:
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474 </inputs>
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jjohnson
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diff changeset
475 <outputs>
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jjohnson
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476 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
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jjohnson
parents:
diff changeset
477 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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jjohnson
parents:
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478 </outputs>
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jjohnson
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diff changeset
479 <tests>
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jjohnson
parents:
diff changeset
480 <test>
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jjohnson
parents:
diff changeset
481 <param name="reference_source_selector" value="history" />
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jjohnson
parents:
diff changeset
482 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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jjohnson
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diff changeset
483 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
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jjohnson
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diff changeset
484 <param name="input_variant" value="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" ftype="vcf" />
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jjohnson
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diff changeset
485 <param name="input_variant_bti" />
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jjohnson
parents:
diff changeset
486 <param name="annotations_type_selector" value="choose" />
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jjohnson
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487 <param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" />
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jjohnson
parents:
diff changeset
488 <param name="additional_annotations" value="0" />
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jjohnson
parents:
diff changeset
489 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
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jjohnson
parents:
diff changeset
490 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
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jjohnson
parents:
diff changeset
491 <param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" />
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jjohnson
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diff changeset
492 <param name="gatk_param_type_selector" value="basic" />
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jjohnson
parents:
diff changeset
493 <output name="output_vcf" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" lines_diff="4" />
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jjohnson
parents:
diff changeset
494 <output name="output_log" file="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains" compare="contains" />
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jjohnson
parents:
diff changeset
495 <param name="comp_rod_bind" value="0" />
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jjohnson
parents:
diff changeset
496 <param name="resource_rod_bind" value="0" />
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jjohnson
parents:
diff changeset
497 <param name="expressions" value="0" />
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jjohnson
parents:
diff changeset
498 <!-- <param name="annotation_group" /> -->
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jjohnson
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499 </test>
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jjohnson
parents:
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500 </tests>
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jjohnson
parents:
diff changeset
501 <help>
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jjohnson
parents:
diff changeset
502 **What it does**
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jjohnson
parents:
diff changeset
503
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jjohnson
parents:
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504 Annotates variant calls with context information. Users can specify which of the available annotations to use.
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jjohnson
parents:
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505
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jjohnson
parents:
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506 For more information on using the VariantAnnotator, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_VariantAnnotator.html&gt;`_.
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jjohnson
parents:
diff changeset
507
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jjohnson
parents:
diff changeset
508 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
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jjohnson
parents:
diff changeset
509
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jjohnson
parents:
diff changeset
510 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
511
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
512 ------
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jjohnson
parents:
diff changeset
513
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
514
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jjohnson
parents:
diff changeset
515 **Inputs**
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jjohnson
parents:
diff changeset
516
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jjohnson
parents:
diff changeset
517 GenomeAnalysisTK: VariantAnnotator accepts a variant input file.
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jjohnson
parents:
diff changeset
518
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jjohnson
parents:
diff changeset
519
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jjohnson
parents:
diff changeset
520 **Outputs**
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jjohnson
parents:
diff changeset
521
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jjohnson
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522 The output is in VCF format.
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jjohnson
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diff changeset
523
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jjohnson
parents:
diff changeset
524
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jjohnson
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525 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
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jjohnson
parents:
diff changeset
526
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jjohnson
parents:
diff changeset
527 -------
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jjohnson
parents:
diff changeset
528
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jjohnson
parents:
diff changeset
529 **Settings**::
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jjohnson
parents:
diff changeset
530
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jjohnson
parents:
diff changeset
531
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532 sampleName The sample (NA-ID) corresponding to the variant input (for non-VCF input only)
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533 annotation One or more specific annotations to apply to variant calls
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534 group One or more classes/groups of annotations to apply to variant calls
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535 expression One or more specific expressions to apply to variant calls; see documentation for more details
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536 useAllAnnotations Use all possible annotations (not for the faint of heart)
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537
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538 ------
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539
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540 **Citation**
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541
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542 For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21478889&gt;`_
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543
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544 Please also site `McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303. Epub 2010 Jul 19. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20644199&gt;`_
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545
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546 If you use this tool in Galaxy, please cite `Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20069535&gt;`_
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547
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548 </help>
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549 </tool>