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view unified_genotyper.xml @ 0:66dd4d4c1743 draft default tip
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| author | devteam |
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| date | Tue, 01 Apr 2014 10:49:12 -0400 |
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<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.6"> <description>SNP and indel caller</description> <requirements> <requirement type="package" version="1.4">gatk</requirement> <requirement type="package" version="0.1.18">samtools</requirement> </requirements> <macros> <import>gatk_macros.xml</import> </macros> <command interpreter="python">gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" #for $i, $input_bam in enumerate( $reference_source.input_bams ): -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}" #if str( $input_bam.input_bam.metadata.bam_index ) != "None": -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index #end if #end for -p 'java -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" --num_threads \${GALAXY_SLOTS:-4} --out "${output_vcf}" --metrics_file "${output_metrics}" -et "NO_ET" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" #end if --genotype_likelihoods_model "${genotype_likelihoods_model}" --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}" --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}" ' #set $rod_binding_names = dict() #for $rod_binding in $rod_bind: #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name #else #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector #end if #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 -d "--dbsnp:${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[$rod_bind_name]}" #end for #include source=$standard_gatk_options# ##start analysis specific options #if $analysis_param_type.analysis_param_type_selector == "advanced": -p ' --p_nonref_model "${analysis_param_type.p_nonref_model}" --heterozygosity "${analysis_param_type.heterozygosity}" --pcr_error_rate "${analysis_param_type.pcr_error_rate}" --genotyping_mode "${analysis_param_type.genotyping_mode_type.genotyping_mode}" #if str( $analysis_param_type.genotyping_mode_type.genotyping_mode ) == 'GENOTYPE_GIVEN_ALLELES': --alleles "${analysis_param_type.genotyping_mode_type.input_alleles_rod}" #end if --output_mode "${analysis_param_type.output_mode}" ${analysis_param_type.compute_SLOD} --min_base_quality_score "${analysis_param_type.min_base_quality_score}" --max_deletion_fraction "${analysis_param_type.max_deletion_fraction}" --max_alternate_alleles "${analysis_param_type.max_alternate_alleles}" --min_indel_count_for_genotyping "${analysis_param_type.min_indel_count_for_genotyping}" --indel_heterozygosity "${analysis_param_type.indel_heterozygosity}" --indelGapContinuationPenalty "${analysis_param_type.indelGapContinuationPenalty}" --indelGapOpenPenalty "${analysis_param_type.indelGapOpenPenalty}" --indelHaplotypeSize "${analysis_param_type.indelHaplotypeSize}" ${analysis_param_type.doContextDependentGapPenalties} #if str( $analysis_param_type.annotation ) != "None": #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','): --annotation "${annotation}" #end for #end if #for $additional_annotation in $analysis_param_type.additional_annotations: --annotation "${additional_annotation.additional_annotation_name}" #end for #if str( $analysis_param_type.group ) != "None": #for $group in str( $analysis_param_type.group ).split( ','): --group "${group}" #end for #end if #if str( $analysis_param_type.exclude_annotations ) != "None": #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','): --excludeAnnotation "${annotation}" #end for #end if ${analysis_param_type.multiallelic} ' ## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': ## -p '--annotation "SnpEff"' ## -d "--snpEffFile:${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}" ## #else: ## -p '--excludeAnnotation "SnpEff"' ## #end if #end if </command> <inputs> <conditional name="reference_source"> <expand macro="reference_source_selector_param" /> <when value="cached"> <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> <param name="input_bam" type="data" format="bam" label="BAM file"> <validator type="unspecified_build" /> <validator type="dataset_metadata_in_data_table" table_name="gatk_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 --> </param> </repeat> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> <options from_data_table="gatk_picard_indexes"> <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> <!-- FIX ME!!!! --> <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> <param name="input_bam" type="data" format="bam" label="BAM file" > </param> </repeat> <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> </when> </conditional> <repeat name="rod_bind" title="Binding for reference-ordered data" help="-D,--dbsnp &lt;dbsnp&gt;"> <conditional name="rod_bind_type"> <param name="rod_bind_type_selector" type="select" label="Binding Type"> <option value="dbsnp" selected="True">dbSNP</option> <option value="snps">SNPs</option> <option value="indels">INDELs</option> <option value="custom">Custom</option> </param> <when value="dbsnp"> <param name="input_rod" type="data" format="vcf" label="ROD file" /> </when> <when value="snps"> <param name="input_rod" type="data" format="vcf" label="ROD file" /> </when> <when value="indels"> <param name="input_rod" type="data" format="vcf" label="ROD file" /> </when> <when value="custom"> <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> <param name="input_rod" type="data" format="vcf" label="ROD file" /> </when> </conditional> </repeat> <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ" help="-glm,--genotype_likelihoods_model &lt;genotype_likelihoods_model&gt;"> <option value="BOTH" selected="True">BOTH</option> <option value="SNP">SNP</option> <option value="INDEL">INDEL</option> </param> <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;" /> <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;" /> <expand macro="gatk_param_type_conditional" /> <expand macro="analysis_type_conditional"> <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;"> <option value="EXACT" selected="True">EXACT</option> <option value="GRID_SEARCH">GRID_SEARCH</option> </param> <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;" /> <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;" /> <conditional name="genotyping_mode_type"> <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;"> <option value="DISCOVERY" selected="True">DISCOVERY</option> <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option> </param> <when value="DISCOVERY"> <!-- Do nothing here --> </when> <when value="GENOTYPE_GIVEN_ALLELES"> <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &lt;alleles&gt;" /> </when> </conditional> <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;"> <option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option> <option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option> <option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option> </param> <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" help="--computeSLOD" /> <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;" /> <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;)" /> <param name="max_alternate_alleles" type="integer" value="5" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles &lt;max_alternate_alleles&gt;" /> <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;" /> <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;)"/> <param name="indelGapContinuationPenalty" type="float" value="10.0" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty" /> <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" help="--indelGapOpenPenalty" /> <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" help="--indelHaplotypeSize" /> <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" help="--doContextDependentGapPenalties" /> <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;"> <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> <options from_data_table="gatk_annotations"> <filter type="multiple_splitter" column="tools_valid_for" separator=","/> <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> </options> </param> <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;"> <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> </repeat> <!-- <conditional name="snpEff_rod_bind_type"> <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file"> <option value="set_snpEff">Set snpEff</option> <option value="exclude_snpEff" selected="True">Don't set snpEff</option> </param> <when value="exclude_snpEff"> </when> <when value="set_snpEff"> <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" /> <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/> </when> </conditional> --> <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups" help="-G,--group &lt;group&gt;"> <option value="RodRequiringAnnotation">RodRequiringAnnotation</option> <option value="Standard">Standard</option> <option value="Experimental">Experimental</option> <option value="WorkInProgress">WorkInProgress</option> <option value="RankSumTest">RankSumTest</option> <!-- <option value="none">none</option> --> </param> <!-- <param name="family_string" type="text" value="" label="Family String"/> --> <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" > <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> <options from_data_table="gatk_annotations"> <filter type="multiple_splitter" column="tools_valid_for" separator=","/> <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> </options> </param> <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" /> </expand> </inputs> <outputs> <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" /> <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" /> <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> </outputs> <trackster_conf/> <tests> <test> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="phiX.fasta" ftype="fasta" /> <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /> <param name="rod_bind_type_selector" value="dbsnp" /> <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> <param name="standard_min_confidence_threshold_for_calling" value="0" /> <param name="standard_min_confidence_threshold_for_emitting" value="4" /> <param name="gatk_param_type_selector" value="basic" /> <param name="analysis_param_type_selector" value="advanced" /> <param name="genotype_likelihoods_model" value="BOTH" /> <param name="p_nonref_model" value="EXACT" /> <param name="heterozygosity" value="0.001" /> <param name="pcr_error_rate" value="0.0001" /> <param name="genotyping_mode" value="DISCOVERY" /> <param name="output_mode" value="EMIT_ALL_CONFIDENT_SITES" /> <param name="compute_SLOD" /> <param name="min_base_quality_score" value="17" /> <param name="max_deletion_fraction" value="-1" /> <param name="min_indel_count_for_genotyping" value="2" /> <param name="indel_heterozygosity" value="0.000125" /> <param name="indelGapContinuationPenalty" value="10" /> <param name="indelGapOpenPenalty" value="3" /> <param name="indelHaplotypeSize" value="80" /> <param name="doContextDependentGapPenalties" /> <!-- <param name="annotation" value="" /> <param name="group" value="" /> --> <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="4" /> <output name="output_metrics" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics" /> <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains" /> </test> </tests> <help> **What it does** 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. For more information on the GATK Unified Genotyper, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Unified_genotyper>`_. To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_. If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_. ------ **Inputs** GenomeAnalysisTK: UnifiedGenotyper accepts an aligned BAM input file. **Outputs** The output is in VCF format. Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats. ------- **Settings**:: 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) p_nonref_model Non-reference probability calculation model to employ -- EXACT is the default option, while GRID_SEARCH is also available. (EXACT|GRID_SEARCH) heterozygosity Heterozygosity value used to compute prior likelihoods for any locus pcr_error_rate The PCR error rate to be used for computing fragment-based likelihoods genotyping_mode Should we output confident genotypes (i.e. including ref calls) or just the variants? (DISCOVERY|GENOTYPE_GIVEN_ALLELES) 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) standard_min_confidence_threshold_for_calling The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called 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) noSLOD If provided, we will not calculate the SLOD min_base_quality_score Minimum base quality required to consider a base for calling 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] min_indel_count_for_genotyping Minimum number of consensus indels required to trigger genotyping run indel_heterozygosity Heterozygosity for indel calling indelGapContinuationPenalty Indel gap continuation penalty indelGapOpenPenalty Indel gap open penalty indelHaplotypeSize Indel haplotype size doContextDependentGapPenalties Vary gap penalties by context indel_recal_file Filename for the input covariates table recalibration .csv file - EXPERIMENTAL, DO NO USE indelDebug Output indel debug info out File to which variants should be written annotation One or more specific annotations to apply to variant calls group One or more classes/groups of annotations to apply to variant calls @CITATION_SECTION@ </help> </tool>