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1 <tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="0.0.7">
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2 <description>SNP and indel caller</description>
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3 <expand macro="requirements" />
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4 <macros>
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5 <import>gatk2_macros.xml</import>
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6 </macros>
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7 <command interpreter="python">
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8 gatk2_wrapper.py
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9 --stdout "${output_log}"
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10 #for $i, $input_bam in enumerate( $reference_source.input_bams ):
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11 -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
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12 #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
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13 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
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14 #end if
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15 #end for
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16 -p '
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17 @JAR_PATH@
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18 -T "UnifiedGenotyper"
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19 @THREADS@
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20 --out "${output_vcf}"
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21 --metrics_file "${output_metrics}"
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22 \$GATK2_SITE_OPTIONS
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23
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24 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
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25 --num_cpu_threads_per_data_thread 6
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26
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27 #if $reference_source.reference_source_selector != "history":
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28 -R "${reference_source.ref_file.fields.path}"
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29 #end if
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30 --genotype_likelihoods_model "${genotype_likelihoods_model}"
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31 --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}"
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32 --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}"
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33 '
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34 #set $rod_binding_names = dict()
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35 #for $rod_binding in $rod_bind:
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36 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
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37 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
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38 #else
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39 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
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40 #end if
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41 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
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42 -d "--dbsnp:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
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43 #end for
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44
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45 #include source=$standard_gatk_options#
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46 ##start analysis specific options
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47 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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48 -p '
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49 --p_nonref_model "${analysis_param_type.p_nonref_model}"
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50 --heterozygosity "${analysis_param_type.heterozygosity}"
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51 --pcr_error_rate "${analysis_param_type.pcr_error_rate}"
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52 --genotyping_mode "${analysis_param_type.genotyping_mode_type.genotyping_mode}"
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53 #if str( $analysis_param_type.genotyping_mode_type.genotyping_mode ) == 'GENOTYPE_GIVEN_ALLELES':
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54 --alleles "${analysis_param_type.genotyping_mode_type.input_alleles_rod}"
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55 #end if
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56 --output_mode "${analysis_param_type.output_mode}"
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57 ${analysis_param_type.compute_SLOD}
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58 --min_base_quality_score "${analysis_param_type.min_base_quality_score}"
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59 --max_deletion_fraction "${analysis_param_type.max_deletion_fraction}"
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60 --max_alternate_alleles "${analysis_param_type.max_alternate_alleles}"
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61 --min_indel_count_for_genotyping "${analysis_param_type.min_indel_count_for_genotyping}"
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62 --indel_heterozygosity "${analysis_param_type.indel_heterozygosity}"
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63 --indelGapContinuationPenalty "${analysis_param_type.indelGapContinuationPenalty}"
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64 --indelGapOpenPenalty "${analysis_param_type.indelGapOpenPenalty}"
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65 --indelHaplotypeSize "${analysis_param_type.indelHaplotypeSize}"
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66 ${analysis_param_type.doContextDependentGapPenalties}
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67 #if str( $analysis_param_type.annotation ) != "None":
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68 #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','):
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69 --annotation "${annotation}"
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70 #end for
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71 #end if
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72 #for $additional_annotation in $analysis_param_type.additional_annotations:
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73 --annotation "${additional_annotation.additional_annotation_name}"
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74 #end for
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75 #if str( $analysis_param_type.group ) != "None":
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76 #for $group in str( $analysis_param_type.group ).split( ','):
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77 --group "${group}"
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78 #end for
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79 #end if
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80 #if str( $analysis_param_type.exclude_annotations ) != "None":
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81 #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','):
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82 --excludeAnnotation "${annotation}"
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83 #end for
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84 #end if
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85 ${analysis_param_type.multiallelic}
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86 #if str( $analysis_param_type.sample_ploidy ) != '':
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87 --sample_ploidy "$analysis_param_type.sample_ploidy"
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88 #end if
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89 '
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90 ## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
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91 ## -p '--annotation "SnpEff"'
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92 ## -d "--snpEffFile:${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod}" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name}"
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93 ## #else:
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94 ## -p '--excludeAnnotation "SnpEff"'
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95 ## #end if
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96 #end if
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97 </command>
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98 <inputs>
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99 <conditional name="reference_source">
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100 <expand macro="reference_source_selector_param" />
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101 <when value="cached">
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102 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;">
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103 <param name="input_bam" type="data" format="bam" label="BAM file">
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104 <validator type="unspecified_build" />
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105 <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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106 </param>
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107 </repeat>
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108 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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109 <options from_data_table="gatk2_picard_indexes">
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110 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
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111 </options>
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112 <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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113 </param>
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114 </when>
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115 <when value="history"> <!-- FIX ME!!!! -->
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116 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;">
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117 <param name="input_bam" type="data" format="bam" label="BAM file" >
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118 </param>
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119 </repeat>
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120 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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121 </when>
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122 </conditional>
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123
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124 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-D,--dbsnp &lt;dbsnp&gt;">
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125 <conditional name="rod_bind_type">
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126 <param name="rod_bind_type_selector" type="select" label="Binding Type">
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127 <option value="dbsnp" selected="True">dbSNP</option>
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128 <option value="snps">SNPs</option>
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129 <option value="indels">INDELs</option>
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130 <option value="custom">Custom</option>
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131 </param>
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132 <when value="dbsnp">
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133 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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134 </when>
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135 <when value="snps">
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136 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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137 </when>
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138 <when value="indels">
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139 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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140 </when>
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141 <when value="custom">
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142 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
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143 <param name="input_rod" type="data" format="vcf" label="ROD file" />
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144 </when>
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145 </conditional>
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146 </repeat>
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147
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148 <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ" help="-glm,--genotype_likelihoods_model &lt;genotype_likelihoods_model&gt;">
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149 <option value="BOTH" selected="True">BOTH</option>
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150 <option value="SNP">SNP</option>
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151 <option value="INDEL">INDEL</option>
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152 </param>
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153
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154 <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" help="-stand_call_conf,--standard_min_confidence_threshold_for_calling &lt;standard_min_confidence_threshold_for_calling&gt;" />
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155 <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" help="-stand_emit_conf,--standard_min_confidence_threshold_for_emitting &lt;standard_min_confidence_threshold_for_emitting&gt;" />
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156
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157
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158 <expand macro="gatk_param_type_conditional" />
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159
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160 <expand macro="analysis_type_conditional">
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161 <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ" help="-pnrm,--p_nonref_model &lt;p_nonref_model&gt;">
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162 <option value="EXACT_GENERAL_PLOIDY" selected="True">EXACT_GENERAL_PLOIDY (supports any sample ploidy)</option>
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163 <option value="EXACT_REFERENCE">EXACT_REFERENCE (multi-allelic EXACT model. Extremely slow for many alternate alleles)</option>
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164 </param>
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165 <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" help="-hets,--heterozygosity &lt;heterozygosity&gt;" />
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166 <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" help="-pcr_error,--pcr_error_rate &lt;pcr_error_rate&gt;" />
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167 <conditional name="genotyping_mode_type">
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168 <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping" help="-gt_mode,--genotyping_mode &lt;genotyping_mode&gt;">
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169 <option value="DISCOVERY" selected="True">DISCOVERY</option>
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170 <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option>
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171 </param>
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172 <when value="DISCOVERY">
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173 <!-- Do nothing here -->
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174 </when>
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175 <when value="GENOTYPE_GIVEN_ALLELES">
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176 <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &lt;alleles&gt;" />
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177 </when>
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178 </conditional>
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179 <param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?" help="-out_mode,--output_mode &lt;output_mode&gt;">
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180 <option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option>
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181 <option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option>
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182 <option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option>
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183 </param>
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184 <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" help="--computeSLOD" />
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185 <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" help="-mbq,--min_base_quality_score &lt;min_base_quality_score&gt;" />
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186 <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to < 0 or > 1 (-deletions,--max_deletion_fraction &lt;max_deletion_fraction&gt;)" />
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187 <param name="max_alternate_alleles" type="integer" value="6" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles &lt;max_alternate_alleles&gt;" />
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188 <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" help="-minIndelCnt,--min_indel_count_for_genotyping &lt;min_indel_count_for_genotyping&gt;" />
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189 <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125 (-indelHeterozygosity,--indel_heterozygosity &lt;indel_heterozygosity&gt;)"/>
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190 <param name="indelGapContinuationPenalty" type="integer" value="10" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty">
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191 <help>Indel gap continuation penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10.</help>
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192 <validator type="in_range" message="value between 0 and 255" min="0" max="255"/>
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193 </param>
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194 <param name="indelGapOpenPenalty" type="integer" value="45" label="Indel gap open penalty" help="--indelGapOpenPenalty" >
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195 <help>Indel gap open penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10.</help>
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196 <validator type="in_range" message="value between 0 and 255" min="0" max="255"/>
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197 </param>
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198 <!-- indelHaplotypeSize - Gone in GATK 2.4? -->
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199 <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" help="--indelHaplotypeSize" />
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200 <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" help="--doContextDependentGapPenalties" />
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201 <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;">
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202 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
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203 <options from_data_table="gatk2_annotations">
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204 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
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205 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
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206 </options>
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207 </param>
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208 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;">
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209 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
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210 </repeat>
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211 <!--
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212 <conditional name="snpEff_rod_bind_type">
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213 <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file">
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214 <option value="set_snpEff">Set snpEff</option>
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215 <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
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216 </param>
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217 <when value="exclude_snpEff">
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218 </when>
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219 <when value="set_snpEff">
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220 <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
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221 <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
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222 </when>
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223 </conditional>
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224 -->
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225 <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups" help="-G,--group &lt;group&gt;">
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226 <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
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227 <option value="Standard">Standard</option>
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228 <option value="Experimental">Experimental</option>
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229 <option value="WorkInProgress">WorkInProgress</option>
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230 <option value="RankSumTest">RankSumTest</option>
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231 <!-- <option value="none">none</option> -->
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232 </param>
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233 <!-- <param name="family_string" type="text" value="" label="Family String"/> -->
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234 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" >
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235 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
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236 <options from_data_table="gatk2_annotations">
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237 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
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238 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
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239 </options>
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240 </param>
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241 <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" />
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242 </expand>
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243 </inputs>
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244 <outputs>
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245 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" />
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246 <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" />
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247 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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248 </outputs>
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249 <trackster_conf/>
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250 <tests>
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251 <test>
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252 <param name="reference_source_selector" value="history" />
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253 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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254 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
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255 <param name="rod_bind_type_selector" value="dbsnp" />
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256 <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
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257 <param name="standard_min_confidence_threshold_for_calling" value="0" />
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258 <param name="standard_min_confidence_threshold_for_emitting" value="4" />
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259 <param name="gatk_param_type_selector" value="basic" />
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260 <param name="analysis_param_type_selector" value="advanced" />
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261 <param name="genotype_likelihoods_model" value="BOTH" />
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262 <param name="p_nonref_model" value="EXACT" />
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263 <param name="heterozygosity" value="0.001" />
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264 <param name="pcr_error_rate" value="0.0001" />
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265 <param name="genotyping_mode" value="DISCOVERY" />
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266 <param name="output_mode" value="EMIT_ALL_CONFIDENT_SITES" />
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267 <param name="compute_SLOD" />
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268 <param name="min_base_quality_score" value="17" />
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269 <param name="max_deletion_fraction" value="-1" />
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270 <param name="min_indel_count_for_genotyping" value="2" />
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271 <param name="indel_heterozygosity" value="0.000125" />
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272 <param name="indelGapContinuationPenalty" value="10" />
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273 <param name="indelGapOpenPenalty" value="3" />
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274 <param name="indelHaplotypeSize" value="80" />
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275 <param name="doContextDependentGapPenalties" />
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276 <!-- <param name="annotation" value="" />
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277 <param name="group" value="" /> -->
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278 <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="4" />
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279 <output name="output_metrics" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics" />
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280 <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains" />
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281 </test>
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282 </tests>
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283 <help>
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284 **What it does**
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285
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286 A variant caller which unifies the approaches of several disparate callers. Works for single-sample and multi-sample data. The user can choose from several different incorporated calculation models.
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287
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288 For more information on the GATK Unified Genotyper, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html>`_.
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289
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290 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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291
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292 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.
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293
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294 ------
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295
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296 **Inputs**
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297
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298 GenomeAnalysisTK: UnifiedGenotyper accepts an aligned BAM input file.
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299
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300
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301 **Outputs**
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302
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303 The output is in VCF format.
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304
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305
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306 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats.
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307
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308 -------
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309
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310 **Settings**::
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311
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312 genotype_likelihoods_model Genotype likelihoods calculation model to employ -- BOTH is the default option, while INDEL is also available for calling indels and SNP is available for calling SNPs only (SNP|INDEL|BOTH)
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313 p_nonref_model Non-reference probability calculation model to employ -- EXACT_GENERAL_PLOIDY is the default option, while EXACT_REFERENCE is also available. (EXACT_INDEPENDENT,EXACT_REFERENCE,EXACT_ORIGINAL,EXACT_GENERAL_PLOIDY)
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314 heterozygosity Heterozygosity value used to compute prior likelihoods for any locus
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315 pcr_error_rate The PCR error rate to be used for computing fragment-based likelihoods
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316 genotyping_mode Should we output confident genotypes (i.e. including ref calls) or just the variants? (DISCOVERY|GENOTYPE_GIVEN_ALLELES)
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317 output_mode Should we output confident genotypes (i.e. including ref calls) or just the variants? (EMIT_VARIANTS_ONLY|EMIT_ALL_CONFIDENT_SITES|EMIT_ALL_SITES)
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318 standard_min_confidence_threshold_for_calling The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called
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319 standard_min_confidence_threshold_for_emitting The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)
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320 noSLOD If provided, we will not calculate the SLOD
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321 min_base_quality_score Minimum base quality required to consider a base for calling
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322 max_deletion_fraction Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]
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323 min_indel_count_for_genotyping Minimum number of consensus indels required to trigger genotyping run
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324 indel_heterozygosity Heterozygosity for indel calling
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325 indelGapContinuationPenalty Indel gap continuation penalty
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326 indelGapOpenPenalty Indel gap open penalty
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327 indelHaplotypeSize Indel haplotype size
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328 doContextDependentGapPenalties Vary gap penalties by context
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329 indel_recal_file Filename for the input covariates table recalibration .csv file - EXPERIMENTAL, DO NO USE
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330 indelDebug Output indel debug info
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331 out File to which variants should be written
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332 annotation One or more specific annotations to apply to variant calls
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333 group One or more classes/groups of annotations to apply to variant calls
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334
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335 @CITATION_SECTION@
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336 </help>
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337 </tool>
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