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1 <tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.1">
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2 <description>SNP and indel caller</description>
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3 <command interpreter="python">gatk_wrapper.py
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4 --stdout "${output_log}"
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5 #for $i, $input_bam in enumerate( $reference_source.input_bams ):
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6 -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
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7 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
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8 #end for
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9 -p 'java
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10 -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
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11 -T "UnifiedGenotyper"
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12 -o "${output_vcf}"
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13 -et "NO_ET" ##ET no phone home
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14 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
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15 #if $reference_source.reference_source_selector != "history":
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16 -R "${reference_source.ref_file.fields.path}"
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17 #end if
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18 --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}"
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19 --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}"
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20 '
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21 #set $rod_binding_names = dict()
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22 #if str( $input_dbsnp_rod ) != "None":
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23 -d "-D" "${input_dbsnp_rod}" "${input_dbsnp_rod.ext}" "dbsnp_rod"
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24 #end if
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25 #for $rod_binding in $rod_bind:
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26 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
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27 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
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28 #else
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29 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
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30 #end if
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31 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
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32 -d "-B:${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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33 #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
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34 -p '--rodToIntervalTrackName "${rod_bind_name}"'
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35 #end if
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36 #end for
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37
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38 ##start standard gatk options
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39 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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40 #for $sample_metadata in $gatk_param_type.sample_metadata:
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41 -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
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42 #end for
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43 #for $read_filter in $gatk_param_type.read_filter:
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44 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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45 ###raise Exception( str( dir( $read_filter ) ) )
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46 #for $name, $param in $read_filter.read_filter_type.iteritems():
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47 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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48 --${name} "${param}"
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49 #end if
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50 #end for
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51 '
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52 #end for
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53 #if str( $gatk_param_type.input_intervals ) != "None":
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54 -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
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55 #end if
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56 #if str( $gatk_param_type.input_exclude_intervals ) != "None":
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57 -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
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58 #end if
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59
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60 -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
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61
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62 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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63 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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64 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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65 #end if
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66 -p '
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67 --baq "${gatk_param_type.baq}"
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68 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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69 ${gatk_param_type.use_original_qualities}
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70 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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71 --validation_strictness "${gatk_param_type.validation_strictness}"
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72 --interval_merging "${gatk_param_type.interval_merging}"
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73 '
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74 #if str( $gatk_param_type.read_group_black_list ) != "None":
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75 -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
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76 #end if
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77 #end if
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78 #if $reference_source.reference_source_selector == "history":
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79 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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80 #end if
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81 ##end standard gatk options
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82 ##start analysis specific options
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83 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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84 -p '
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85 --genotype_likelihoods_model "${analysis_param_type.genotype_likelihoods_model}"
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86 --p_nonref_model "${analysis_param_type.p_nonref_model}"
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87 --heterozygosity "${analysis_param_type.heterozygosity}"
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88 --pcr_error_rate "${analysis_param_type.pcr_error_rate}"
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89 --genotyping_mode "${analysis_param_type.genotyping_mode}"
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90 --output_mode "${analysis_param_type.output_mode}"
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91 ${analysis_param_type.noSLOD}
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92 --min_base_quality_score "${analysis_param_type.min_base_quality_score}"
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93 --min_mapping_quality_score "${analysis_param_type.min_mapping_quality_score}"
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94 --max_deletion_fraction "${analysis_param_type.max_deletion_fraction}"
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95 --min_indel_count_for_genotyping "${analysis_param_type.min_indel_count_for_genotyping}"
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96 --indel_heterozygosity "${analysis_param_type.indel_heterozygosity}"
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97 --indelGapContinuationPenalty "${analysis_param_type.indelGapContinuationPenalty}"
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98 --indelGapOpenPenalty "${analysis_param_type.indelGapOpenPenalty}"
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99 --indelHaplotypeSize "${analysis_param_type.indelHaplotypeSize}"
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100 ${analysis_param_type.doContextDependentGapPenalties}
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101 #if $analysis_param_type.annotation.value:
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102 #for $annotation in $analysis_param_type.annotation.value:
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103 --annotation "${annotation}"
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104 #end for
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105 #end if
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106 #if $analysis_param_type.group.value:
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107 #for $group in $analysis_param_type.group.value:
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108 --group "${group}"
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109 #end for
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110 #end if
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111 '
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112 #end if
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113 </command>
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114 <inputs>
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115 <conditional name="reference_source">
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116 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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117 <option value="cached">Locally cached</option>
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118 <option value="history">History</option>
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119 </param>
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120 <when value="cached">
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121 <repeat name="input_bams" title="Sample BAM file" min="1">
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122 <param name="input_bam" type="data" format="bam" label="BAM file">
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123 <validator type="unspecified_build" />
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124 <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
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125 </param>
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126 </repeat>
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127 <param name="ref_file" type="select" label="Using reference genome">
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128 <options from_data_table="picard_indexes">
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129 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
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130 </options>
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131 </param>
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132 </when>
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133 <when value="history"> <!-- FIX ME!!!! -->
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134 <repeat name="input_bams" title="Sample BAM file" min="1">
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135 <param name="input_bam" type="data" format="bam" label="BAM file" />
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136 </repeat>
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137 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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138 </when>
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139 </conditional>
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140
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141 <param name="input_dbsnp_rod" type="data" format="gatk_dbsnp" optional="True" label="dbSNP reference ordered data (ROD)" />
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142 <repeat name="rod_bind" title="Binding for reference-ordered data">
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143 <conditional name="rod_bind_type">
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144 <param name="rod_bind_type_selector" type="select" label="Binding Type">
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145 <option value="snps" selected="True">SNPs</option>
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146 <option value="indels">INDELs</option>
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147 <option value="custom">Custom</option>
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148 </param>
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149 <when value="snps">
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150 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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151 <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
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152 </when>
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153 <when value="indels">
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154 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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155 <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
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156 </when>
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157 <when value="custom">
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158 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
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159 <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
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160 <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
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161 </when>
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162 </conditional>
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163 </repeat>
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164
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165 <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" />
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166 <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)" />
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167
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168
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169 <conditional name="gatk_param_type">
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170 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
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171 <option value="basic" selected="True">Basic</option>
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172 <option value="advanced">Advanced</option>
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173 </param>
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174 <when value="basic">
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175 <!-- Do nothing here -->
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176 </when>
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177 <when value="advanced">
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178 <repeat name="sample_metadata" title="Sample Metadata">
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179 <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
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180 </repeat>
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181 <repeat name="read_filter" title="Read Filter">
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182 <conditional name="read_filter_type">
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183 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
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184 <option value="MaxReadLength" selected="True">MaxReadLength</option>
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185 <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
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186 </param>
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187 <when value="ZeroMappingQualityRead">
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188 <!-- no extra options -->
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189 </when>
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190 <when value="MaxReadLength">
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191 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
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192 </when>
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193 </conditional>
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194 </repeat>
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195 <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
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196 <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
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197
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198 <param name="BTI_merge_rule" type="select" label="BTI merge rule">
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199 <option value="UNION" selected="True">UNION</option>
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200 <option value="INTERSECTION">INTERSECTION</option>
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201 </param>
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202
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203 <conditional name="downsampling_type">
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204 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
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205 <option value="NONE" selected="True">NONE</option>
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206 <option value="ALL_READS">ALL_READS</option>
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207 <option value="BY_SAMPLE">BY_SAMPLE</option>
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208 </param>
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209 <when value="NONE">
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210 <!-- no more options here -->
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211 </when>
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212 <when value="ALL_READS">
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213 <conditional name="downsample_to_type">
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214 <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
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215 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
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216 <option value="downsample_to_coverage">Downsample by Coverage</option>
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217 </param>
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218 <when value="downsample_to_fraction">
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219 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
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220 </when>
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221 <when value="downsample_to_coverage">
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222 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
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223 </when>
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224 </conditional>
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225 </when>
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226 <when value="BY_SAMPLE">
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227 <conditional name="downsample_to_type">
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228 <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
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229 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
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230 <option value="downsample_to_coverage">Downsample by Coverage</option>
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231 </param>
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232 <when value="downsample_to_fraction">
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233 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
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234 </when>
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235 <when value="downsample_to_coverage">
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236 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
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237 </when>
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238 </conditional>
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239 </when>
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240 </conditional>
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241 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
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242 <option value="OFF" selected="True">OFF</option>
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243 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
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244 <option value="RECALCULATE">RECALCULATE</option>
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245 </param>
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246 <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
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247 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
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248 <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
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249 <param name="validation_strictness" type="select" label="How strict should we be with validation">
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250 <option value="STRICT" selected="True">STRICT</option>
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251 <option value="LENIENT">LENIENT</option>
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252 <option value="SILENT">SILENT</option>
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253 </param>
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254 <param name="interval_merging" type="select" label="Interval merging rule">
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255 <option value="ALL" selected="True">ALL</option>
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256 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
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257 </param>
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258 <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
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259 </when>
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260 </conditional>
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261
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262 <conditional name="analysis_param_type">
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263 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
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264 <option value="basic" selected="True">Basic</option>
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265 <option value="advanced">Advanced</option>
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266 </param>
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267 <when value="basic">
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268 <!-- Do nothing here -->
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269 </when>
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270 <when value="advanced">
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271 <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ">
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272 <option value="BOTH" selected="True">BOTH</option>
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273 <option value="SNP">SNP</option>
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274 <option value="INDEL">INDEL</option>
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275 </param>
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276 <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ">
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277 <option value="EXACT" selected="True">EXACT</option>
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278 <option value="GRID_SEARCH">GRID_SEARCH</option>
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279 </param>
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280 <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" />
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281 <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" />
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282 <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping">
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283 <option value="DISCOVERY" selected="True">DISCOVERY</option>
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284 <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option>
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285 </param>
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286 <param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?">
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287 <option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option>
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288 <option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option>
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289 <option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option>
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290 </param>
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291 <param name="noSLOD" type="boolean" truevalue="--noSLOD" falsevalue="" label="Do not calculate the SLOD" />
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292 <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" />
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293 <param name="min_mapping_quality_score" type="integer" value="20" label="Minimum read mapping quality required to consider a read for calling" />
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294 <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" />
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295 <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" />
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296 <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125"/>
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297 <param name="indelGapContinuationPenalty" type="float" value="10.0" label="Indel gap continuation penalty" />
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298 <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" />
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299 <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" />
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300 <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" />
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301 <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types">
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302 <option value="AlleleBalance">AlleleBalance</option>
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303 <option value="BaseQualityRankSumTest">BaseQualityRankSumTest</option>
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304 <option value="DepthOfCoverage">DepthOfCoverage</option>
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305 <option value="HomopolymerRun">HomopolymerRun</option>
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306 <option value="MappingQualityRankSumTest">MappingQualityRankSumTest</option>
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307 <option value="MappingQualityZero">MappingQualityZero</option>
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308 <option value="QualByDepth">QualByDepth</option>
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309 <option value="RMSMappingQuality">RMSMappingQuality</option>
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310 <option value="SpanningDeletions">SpanningDeletions</option>
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311 <option value="HaplotypeScore">HaplotypeScore</option>
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312 </param>
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313 <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups">
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314 <option value="Standard">Standard</option>
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315 <option value="Experimental">Experimental</option>
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316 <option value="WorkInProgress">WorkInProgress</option>
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317 <!-- <option value="none">none</option> -->
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318 </param>
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319 </when>
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320 </conditional>
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321 </inputs>
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322 <outputs>
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323 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" />
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324 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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325 </outputs>
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326 <tests>
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327 <test>
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328 <param name="reference_source_selector" value="history" />
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329 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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330 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
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331 <param name="input_dbsnp_rod" />
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332 <param name="rod_bind_type_selector" value="snps" />
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333 <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" />
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334 <param name="rodToIntervalTrackName" />
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335 <param name="standard_min_confidence_threshold_for_calling" value="4" />
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336 <param name="standard_min_confidence_threshold_for_emitting" value="4" />
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337 <param name="gatk_param_type_selector" value="basic" />
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338 <param name="analysis_param_type_selector" value="advanced" />
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339 <param name="genotype_likelihoods_model" value="BOTH" />
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340 <param name="p_nonref_model" value="EXACT" />
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341 <param name="heterozygosity" value="0.001" />
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342 <param name="pcr_error_rate" value="0.0001" />
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343 <param name="genotyping_mode" value="DISCOVERY" />
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344 <param name="output_mode" value="EMIT_ALL_CONFIDENT_SITES" />
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345 <param name="noSLOD" />
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346 <param name="min_base_quality_score" value="17" />
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347 <param name="min_mapping_quality_score" value="20" />
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348 <param name="max_deletion_fraction" value="-1" />
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349 <param name="min_indel_count_for_genotyping" value="2" />
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350 <param name="indel_heterozygosity" value="0.000125" />
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351 <param name="indelGapContinuationPenalty" value="10" />
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352 <param name="indelGapOpenPenalty" value="3" />
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353 <param name="indelHaplotypeSize" value="80" />
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354 <param name="doContextDependentGapPenalties" />
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355 <!-- <param name="annotation" value="" />
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356 <param name="group" value="" /> -->
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357 <output name="output_interval" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="2"/>
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358 <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains"/>
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359 </test>
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360 </tests>
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361 <help>
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362 **What it does**
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363
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364 A variant caller which unifies the approaches of several disparate callers. Works for single-sample and
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365 multi-sample data. The user can choose from several different incorporated calculation models.
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366
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367 ------
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368
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369 Please cite the website "http://addlink.here" as well as:
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370
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371 Add citation here 2011.
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372
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373 ------
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374
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375 **Input formats**
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376
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377 GenomeAnalysisTK: UnifiedGenotyper accepts an aligned BAM input file.
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378
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379 ------
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380
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381 **Outputs**
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382
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383 The output is in VCF format, see http://addlink.here for more details.
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384
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385 -------
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386
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387 **Settings**::
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388
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389 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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390 p_nonref_model Non-reference probability calculation model to employ -- EXACT is the default option, while GRID_SEARCH is also available. (EXACT|GRID_SEARCH)
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391 heterozygosity Heterozygosity value used to compute prior likelihoods for any locus
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392 pcr_error_rate The PCR error rate to be used for computing fragment-based likelihoods
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393 genotyping_mode Should we output confident genotypes (i.e. including ref calls) or just the variants? (DISCOVERY|GENOTYPE_GIVEN_ALLELES)
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394 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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395 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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396 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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397 noSLOD If provided, we will not calculate the SLOD
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398 min_base_quality_score Minimum base quality required to consider a base for calling
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399 min_mapping_quality_score Minimum read mapping quality required to consider a read for calling
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400 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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401 min_indel_count_for_genotyping Minimum number of consensus indels required to trigger genotyping run
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402 indel_heterozygosity Heterozygosity for indel calling
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403 indelGapContinuationPenalty Indel gap continuation penalty
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404 indelGapOpenPenalty Indel gap open penalty
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405 indelHaplotypeSize Indel haplotype size
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406 doContextDependentGapPenalties Vary gap penalties by context
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407 indel_recal_file Filename for the input covariates table recalibration .csv file - EXPERIMENTAL, DO NO USE
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408 indelDebug Output indel debug info
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409 out File to which variants should be written
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410 annotation One or more specific annotations to apply to variant calls
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411 group One or more classes/groups of annotations to apply to variant calls
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412
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413 </help>
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414 </tool>
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