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1 <tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="0.0.7">
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2 <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</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 "${output_log}"
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10 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
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11 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
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12 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
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13 #end if
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14 -p '
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15 @JAR_PATH@
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16 -T "HaplotypeCaller"
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17 -o "${output_vcf}"
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18
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19 \$GATK2_SITE_OPTIONS
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20
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21 @THREADS@
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22
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23 #if $reference_source.reference_source_selector != "history":
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24 -R "${reference_source.ref_file.fields.path}"
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25 #end if
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26 #if str($input_recal) != 'None':
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27 --BQSR "${input_recal}"
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28 #end if
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29 '
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30 #include source=$standard_gatk_options#
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31
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32 ##start analysis specific options
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33 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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34 -p '
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35 #if $analysis_param_type.p_nonref_model.__str__ != "None" and len($analysis_param_type.p_nonref_model.__str__) > 0:
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36 --p_nonref_model $analysis_param_type.p_nonref_model
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37 #end if
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38 #if $analysis_param_type.heterozygosity.__str__.strip() != '':
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39 --heterozygosity $analysis_param_type.heterozygosity
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40 #end if
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41 --genotyping_mode "${analysis_param_type.genotyping_mode_type.genotyping_mode}"
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42 #if str( $analysis_param_type.genotyping_mode_type.genotyping_mode ) == 'GENOTYPE_GIVEN_ALLELES':
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43 --alleles "${analysis_param_type.genotyping_mode_type.input_alleles_rod}"
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44 #end if
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45 #if $analysis_param_type.output_mode.__str__ != "None" and len($analysis_param_type.output_mode.__str__) > 0:
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46 --output_mode $analysis_param_type.output_mode
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47 #end if
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48
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49 ## files
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50 #if str($analysis_param_type.activeRegionIn) != 'None':
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51 --activeRegionIn "$analysis_param_type.activeRegionIn"
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52 #end if
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53 #if str($analysis_param_type.comp) != 'None':
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54 --comp "$analysis_param_type.comp"
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55 #end if
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56 #if str($analysis_param_type.dbsnp) != 'None':
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57 --dbsnp "$analysis_param_type.dbsnp"
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58 #end if
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59 ##
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60 #if str( $analysis_param_type.annotation ) != "None":
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61 #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','):
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62 --annotation "${annotation}"
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63 #end for
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64 #end if
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65 #for $additional_annotation in $analysis_param_type.additional_annotations:
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66 --annotation "${additional_annotation.additional_annotation_name}"
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67 #end for
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68 #if str( $analysis_param_type.group ) != "None":
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69 #for $group in str( $analysis_param_type.group ).split( ','):
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70 --group "${group}"
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71 #end for
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72 #end if
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73 #if str( $analysis_param_type.exclude_annotations ) != "None":
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74 #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','):
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75 --excludeAnnotation "${annotation}"
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76 #end for
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77 #end if
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78
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79 ## value setings
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80 #if $analysis_param_type.contamination_fraction_to_filter.__str__.strip() != '':
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81 --contamination_fraction_to_filter $analysis_param_type.contamination_fraction_to_filter
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82 #end if
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83 #if $analysis_param_type.downsampleRegion.__str__.strip() != '':
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84 --downsampleRegion $analysis_param_type.downsampleRegion
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85 #end if
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86 #if $analysis_param_type.minPruning.__str__.strip() != '':
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87 --minPruning $analysis_param_type.minPruning
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88 #end if
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89 #if $analysis_param_type.standard_min_confidence_threshold_for_calling.__str__.strip() != '':
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90 --standard_min_confidence_threshold_for_calling $analysis_param_type.standard_min_confidence_threshold_for_calling
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91 #end if
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92 #if $analysis_param_type.standard_min_confidence_threshold_for_emitting.__str__.strip() != '':
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93 --standard_min_confidence_threshold_for_emitting $analysis_param_type.standard_min_confidence_threshold_for_emitting
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94 #end if
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95 #if $analysis_param_type.gcpHMM.__str__.strip() != '':
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96 --gcpHMM $analysis_param_type.gcpHMM
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97 #end if
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98 #if $analysis_param_type.max_alternate_alleles.__str__.strip() != '':
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99 --max_alternate_alleles $analysis_param_type.max_alternate_alleles
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100 #end if
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101 ## mode selections
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102 #if $analysis_param_type.genotyping_mode.__str__ != "None" and len($analysis_param_type.genotyping_mode.__str__) > 0:
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103 --genotyping_mode $analysis_param_type.genotyping_mode
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104 #end if
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105 #if $analysis_param_type.pair_hmm_implementation.__str__ != "None" and len($analysis_param_type.pair_hmm_implementation.__str__) > 0:
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106 --pair_hmm_implementation $analysis_param_type.pair_hmm_implementation
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107 #end if
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108 ## optional outputs
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109 #if $analysis_param_type.activeRegionOut:
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110 --activeRegionOut $active_region_out
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111 #end if
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112 #if $analysis_param_type.graphOutput:
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113 --graphOutput $graph_out
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114 #end if
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115 ## flags
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116 $analysis_param_type.useAllelesTrigger
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117 $analysis_param_type.fullHaplotype
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118 $analysis_param_type.genotypeFullActiveRegion
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119 $analysis_param_type.debug
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120 '
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121 #end if
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122 </command>
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123 <inputs>
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124 <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &lt;recal_file&gt;" >
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125 <help>The input covariates table file which enables on-the-fly base quality score recalibration.
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126 Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool.
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127 Please be aware that one should only run recalibration with the covariates file created on the same input bam(s).
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128 </help>
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129 </param>
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130 <conditional name="reference_source">
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131 <expand macro="reference_source_selector_param" />
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132 <when value="cached">
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133 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;">
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134 <validator type="unspecified_build" />
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135 <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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136 </param>
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137 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;" >
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138 <options from_data_table="gatk2_picard_indexes">
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139 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
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140 </options>
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141 <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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142 </param>
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143 </when>
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144 <when value="history">
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145 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" />
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146 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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147 <options>
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148 <filter type="data_meta" key="dbkey" ref="input_bam" />
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149 </options>
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150 </param>
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151 </when>
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152 </conditional>
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153
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154 <expand macro="gatk_param_type_conditional" />
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155
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156 <conditional name="analysis_param_type">
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157 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
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158 <option value="basic" selected="True">Basic</option>
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159 <option value="advanced">Advanced</option>
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160 </param>
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161 <when value="basic">
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162 <!-- Do nothing here -->
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163 </when>
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164 <when value="advanced">
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165
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166 <param name="activeRegionIn" type="data" format="bed,gatk_interval,picard_interval_list,vcf" optional="true" label="activeRegionIn" help="--activeRegionIn / -AR Use this interval list file as the active regions to process"/>
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167 <param name="activeRegionOut" type="boolean" checked="False" truevalue="" falsevalue="" label="activeRegionOut" help="--activeRegionOut / -ARO Output the active region to an interval list file"/>
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168
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169 <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;">
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170 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
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171 <options from_data_table="gatk2_annotations">
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172 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
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173 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
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174 </options>
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175 </param>
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176 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;">
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177 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
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178 </repeat>
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179 <!--
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180 <conditional name="snpEff_rod_bind_type">
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181 <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file">
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182 <option value="set_snpEff">Set snpEff</option>
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183 <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
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184 </param>
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185 <when value="exclude_snpEff">
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186 </when>
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187 <when value="set_snpEff">
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188 <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
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189 <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
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190 </when>
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191 </conditional>
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192 -->
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193 <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups" help="-G,--group &lt;group&gt;">
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194 <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
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195 <option value="Standard">Standard</option>
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196 <option value="Experimental">Experimental</option>
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197 <option value="WorkInProgress">WorkInProgress</option>
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198 <option value="RankSumTest">RankSumTest</option>
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199 <!-- <option value="none">none</option> -->
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200 </param>
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201 <!-- <param name="family_string" type="text" value="" label="Family String"/> -->
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202 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" >
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203 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
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204 <options from_data_table="gatk2_annotations">
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205 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
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206 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
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207 </options>
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208 </param>
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209
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210 <param name="comp" type="data" format="vcf" optional="true" label="comp" help="--comp / -comp comparison VCF file"/>
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211 <param name="contamination_fraction_to_filter" type="float" value="0.05" optional="true" label="contamination_fraction_to_filter" help="--contamination_fraction_to_filter / -contamination Fraction of contamination in sequencing data (for all samples) to aggressively remove">
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212 <validator type="in_range" message="value between 0.00 and 1.00" min="0" max="1"/>
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213 </param>
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214 <param name="dbsnp" type="data" format="vcf" optional="true" label="dbsnp" help="--dbsnp / -D dbSNP file"/>
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215 <param name="debug" type="boolean" checked="False" truevalue="-debug" falsevalue="" label="debug" help="--debug / -debug If specified, print out very verbose debug information about each triggering active region"/>
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216 <param name="downsampleRegion" type="integer" value="1000" optional="true" label="downsampleRegion" help="--downsampleRegion / -dr coverage, per-sample, to downsample each active region to"/>
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217
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218 <conditional name="genotyping_mode_type">
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219 <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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220 <option value="DISCOVERY" selected="True">DISCOVERY</option>
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221 <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option>
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222 </param>
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223 <when value="DISCOVERY">
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224 <!-- Do nothing here -->
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225 </when>
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226 <when value="GENOTYPE_GIVEN_ALLELES">
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227 <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &lt;alleles&gt;" />
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228 </when>
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229 </conditional>
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230
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231
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232 <param name="graphOutput" type="boolean" checked="False" truevalue="" falsevalue="" label="graphOutput" help="--graphOutput / -graph File to which debug assembly graph information should be written"/>
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233 <param name="heterozygosity" type="float" value="0.0010" optional="true" label="heterozygosity" help="--heterozygosity / -hets Heterozygosity value used to compute prior likelihoods for any locus"/>
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234 <param name="minPruning" type="integer" value="1" optional="true" label="minPruning" help="--minPruning / -minPruning The minimum allowed pruning factor in assembly graph. Paths with >= X supporting kmers are pruned from the graph">
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235 <validator type="in_range" message="value between 0 and 127" min="0" max="127"/>
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236 </param>
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237 <param name="output_mode" type="select" optional="true" label="output_mode" help="--output_mode / -out_mode Specifies which type of calls we should output">
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238 <option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option>
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239 <option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option>
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240 <option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option>
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241 </param>
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242 <param name="pair_hmm_implementation" type="select" optional="true" label="pair_hmm_implementation" help="--pair_hmm_implementation / -pairHMM The PairHMM implementation to use for genotype likelihood calculations">
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243 <option value="EXACT">EXACT</option>
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244 <option value="ORIGINAL">ORIGINAL</option>
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245 <option value="CACHING">CACHING</option>
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246 <option value="LOGLESS_CACHING" selected="True">LOGLESS_CACHING</option>
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247 </param>
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248 <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" optional="true" label="standard_min_confidence_threshold_for_calling" help="--standard_min_confidence_threshold_for_calling / -stand_call_conf The minimum phred-scaled confidence threshold at which variants should be called"/>
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249 <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" optional="true" label="standard_min_confidence_threshold_for_emitting" help="--standard_min_confidence_threshold_for_emitting / -stand_emit_conf The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)"/>
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250 <param name="useAllelesTrigger" type="boolean" checked="False" truevalue="-allelesTrigger" falsevalue="" label="useAllelesTrigger" help="--useAllelesTrigger / -allelesTrigger If specified, use additional trigger on variants found in an external alleles file"/>
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251 <param name="fullHaplotype" type="boolean" checked="False" truevalue="-fullHaplotype" falsevalue="" label="fullHaplotype" help="--fullHaplotype / -fullHaplotype If specified, output the full haplotype sequence instead of converting to individual variants w.r.t. the reference"/>
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252 <param name="gcpHMM" type="integer" value="10" optional="true" label="gcpHMM" help="--gcpHMM / -gcpHMM Flat gap continuation penalty for use in the Pair HMM"/>
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253 <param name="genotypeFullActiveRegion" type="boolean" checked="False" truevalue="-genotypeFullActiveRegion" falsevalue="" label="genotypeFullActiveRegion" help="--genotypeFullActiveRegion / -genotypeFullActiveRegion If specified, alternate alleles are considered to be the full active region for the purposes of genotyping"/>
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254 <param name="max_alternate_alleles" type="integer" value="6" optional="true" label="max_alternate_alleles" help="--max_alternate_alleles / -maxAltAlleles Maximum number of alternate alleles to genotype"/>
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255 <param name="p_nonref_model" type="select" optional="true" label="p_nonref_model" help="--p_nonref_model / -pnrm Non-reference probability calculation model to employ">
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256 <option value="EXACT_INDEPENDENT" selected="True">EXACT_INDEPENDENT experimental implementation - for testing only</option>
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257 <option value="EXACT_REFERENCE">EXACT_REFERENCE reference implementation of multi-allelic EXACT model. Extremely slow for many alternate alleles</option>
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258 <option value="EXACT_ORIGINAL">EXACT_ORIGINAL original biallelic exact model, for testing only</option>
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259 <option value="EXACT_GENERAL_PLOIDY">implementation that supports any sample ploidy</option>
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260 </param>
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261
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262 </when>
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263 </conditional>
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264 </inputs>
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265 <outputs>
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266 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" />
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267 <data format="vcf" name="graph_out" label="${tool.name} on ${on_string} graph" >
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268 <filter>analysis_param_type['analysis_param_type_selector'] == "advanced" and analysis_param_type['graphOutput'] == True</filter>
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269 </data>
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270 <data format="vcf" name="active_region_out" label="${tool.name} on ${on_string} activeRegion" >
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271 <filter>analysis_param_type['analysis_param_type_selector'] == "advanced" and analysis_param_type['activeRegionOut'] == True</filter>
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272 </data>
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273 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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274 </outputs>
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275 <tests>
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276 <test>
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277 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" />
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278 <param name="reference_source_selector" value="history" />
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279 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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280 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
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281 <param name="gatk_param_type_selector" value="basic" />
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282 <param name="analysis_param_type_selector" value="basic" />
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283 <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" lines_diff="4" />
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284 <output name="output_log" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains" compare="contains" />
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285 </test>
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286 </tests>
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287 <help>
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288 **What it does**
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289
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290 **HaplotypeCaller**
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291 calls SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region.
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292 Haplotypes are evaluated using an affine gap penalty Pair HMM.
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293
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294 For more information on using read based compression in the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_haplotypecaller_HaplotypeCaller.html>`_.
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295
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296 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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297
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298 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.
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299
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300 ------
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301
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302 **Inputs**
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303
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304 GenomeAnalysisTK: PrintReads accepts aligned BAM files.
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305
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306
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307 **Outputs**
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308
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309 The output is a VCF file with raw, unrecalibrated SNP and indel calls.
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310
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311
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312 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats.
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313
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314 -------
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315
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316 **Settings**::
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317
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318 activeRegionIn Use this interval list file as the active regions to process
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319 activeRegionOut Output the active region to this interval list file
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320 alleles The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES
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321 annotation One or more specific annotations to apply to variant calls
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322 comp comparison VCF file
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323 contamination Fraction of contamination in sequencing data (for all samples) to aggressively remove
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324 dbsnp dbSNP file
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325 debug If specified, print out very verbose debug information about each triggering active region
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326 downsampleRegion coverage, per-sample, to downsample each active region to
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327 excludeAnnotation One or more specific annotations to exclude
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328 genotyping_mode Specifies how to determine the alternate alleles to use for genotyping
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329 graphOutput File to which debug assembly graph information should be written
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330 group One or more classes/groups of annotations to apply to variant calls
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331 heterozygosity Heterozygosity value used to compute prior likelihoods for any locus
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332 minPruning The minimum allowed pruning factor in assembly graph. Paths with less than or equal supporting kmers are pruned from the graph
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333 output_mode Specifies which type of calls we should output
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334 pair_hmm_implementation The PairHMM implementation to use for genotype likelihood calculations
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335 stand_call_conf The minimum phred-scaled confidence threshold at which variants should be called
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336 stand_emit_conf The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)
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337 useAllelesTrigger If specified, use additional trigger on variants found in an external alleles file
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338 fullHaplotype If specified, output the full haplotype sequence instead of converting to individual variants w.r.t. the reference
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339 gcpHMM Flat gap continuation penalty for use in the Pair HMM
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340 genotypeFullActiveRegion If specified, alternate alleles are considered to be the full active region for the purposes of genotyping
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341 max_alternate_alleles Maximum number of alternate alleles to genotype
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342 p_nonref_model Non-reference probability calculation model to employ
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343
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344 ------
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345
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346 @CITATION_SECTION@
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347 </help>
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348 </tool>
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