Mercurial > repos > jjohnson > gatk2
view haplotype_caller.xml @ 29:c511aa6f93da draft
Temporarily use my own copy of samtools until cross dependency support is in release
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 19 Feb 2013 20:59:51 -0600 |
| parents | 6ef8eb568700 |
| children | b99c25b0ad4d |
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<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="0.0.5"> <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</description> <requirements> <requirement type="package" version="2.3">gatk</requirement> <requirement type="package" version="0.1.18">samtools</requirement> </requirements> <command interpreter="python">gatk2_wrapper.py --max_jvm_heap_fraction "1" --stdout "${output_log}" -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" #if str( $reference_source.input_bam.metadata.bam_index ) != "None": -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index #end if -p 'java -jar "\$GATK2_PATH/GenomeAnalysisTK.jar" -T "HaplotypeCaller" -o "${output_vcf}" ## \$GATK2_SITE_OPTIONS ## \$GATK2_NUM_THREADS ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home ##--num_threads 4 ##not supported yet ##-log "${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 #if str($input_recal) != 'None': --BQSR "${input_recal}" #end if ' ##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": #for $pedigree in $gatk_param_type.pedigree: -p '--pedigree "${pedigree.pedigree_file}"' #end for #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: -p '--pedigreeString "${pedigree_string.pedigree_string}"' #end for -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' #for $read_filter in $gatk_param_type.read_filter: -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" ###raise Exception( str( dir( $read_filter ) ) ) #for $name, $param in $read_filter.read_filter_type.iteritems(): #if $name not in [ "__current_case__", "read_filter_type_selector" ]: #if hasattr( $param.input, 'truevalue' ): ${param} #else: --${name} "${param}" #end if #end if #end for ' #end for #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" #end for #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" #end for -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"' -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' #end if -p ' --baq "${gatk_param_type.baq}" --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}" ${gatk_param_type.use_original_qualities} --defaultBaseQualities "${gatk_param_type.default_base_qualities}" --validation_strictness "${gatk_param_type.validation_strictness}" --interval_merging "${gatk_param_type.interval_merging}" ${gatk_param_type.fix_misencoded_quality_scores} ${gatk_param_type.non_deterministic_random_seed} ' #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ): #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file": -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}" #else -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' #end if #end for #end if #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if ##end standard gatk options ##start analysis specific options #if $analysis_param_type.analysis_param_type_selector == "advanced": -p ' #if $analysis_param_type.p_nonref_model.__str__ != "None" and len($analysis_param_type.p_nonref_model.__str__) > 0: --p_nonref_model $analysis_param_type.p_nonref_model #end if #if $analysis_param_type.heterozygosity.__str__.strip() != '': --heterozygosity $analysis_param_type.heterozygosity #end if --genotyping_mode "${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 #if $analysis_param_type.output_mode.__str__ != "None" and len($analysis_param_type.output_mode.__str__) > 0: --output_mode $analysis_param_type.output_mode #end if ## files #if str($analysis_param_type.activeRegionIn) != 'None': --activeRegionIn "$analysis_param_type.activeRegionIn" #end if #if str($analysis_param_type.comp) != 'None': --comp "$analysis_param_type.comp" #end if #if str($analysis_param_type.dbsnp) != 'None': --dbsnp "$analysis_param_type.dbsnp" #end if ## #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 ## value setings #if $analysis_param_type.contamination_fraction_to_filter.__str__.strip() != '': --contamination_fraction_to_filter $analysis_param_type.contamination_fraction_to_filter #end if #if $analysis_param_type.downsampleRegion.__str__.strip() != '': --downsampleRegion $analysis_param_type.downsampleRegion #end if #if $analysis_param_type.minPruning.__str__.strip() != '': --minPruning $analysis_param_type.minPruning #end if #if $analysis_param_type.standard_min_confidence_threshold_for_calling.__str__.strip() != '': --standard_min_confidence_threshold_for_calling $analysis_param_type.standard_min_confidence_threshold_for_calling #end if #if $analysis_param_type.standard_min_confidence_threshold_for_emitting.__str__.strip() != '': --standard_min_confidence_threshold_for_emitting $analysis_param_type.standard_min_confidence_threshold_for_emitting #end if #if $analysis_param_type.gcpHMM.__str__.strip() != '': --gcpHMM $analysis_param_type.gcpHMM #end if #if $analysis_param_type.max_alternate_alleles.__str__.strip() != '': --max_alternate_alleles $analysis_param_type.max_alternate_alleles #end if ## mode selections #if $analysis_param_type.genotyping_mode.__str__ != "None" and len($analysis_param_type.genotyping_mode.__str__) > 0: --genotyping_mode $analysis_param_type.genotyping_mode #end if #if $analysis_param_type.pair_hmm_implementation.__str__ != "None" and len($analysis_param_type.pair_hmm_implementation.__str__) > 0: --pair_hmm_implementation $analysis_param_type.pair_hmm_implementation #end if ## optional outputs #if $analysis_param_type.activeRegionOut: --activeRegionOut $active_region_out #end if #if $analysis_param_type.graphOutput: --graphOutput $graph_out #end if ## flags $analysis_param_type.useAllelesTrigger $analysis_param_type.fullHaplotype $analysis_param_type.genotypeFullActiveRegion $analysis_param_type.debug ' #end if </command> <inputs> <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" help="-BQSR,--BQSR &lt;recal_file&gt;" > <help>The input covariates table file which enables on-the-fly base quality score recalibration. Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool. Please be aware that one should only run recalibration with the covariates file created on the same input bam(s). </help> </param> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> <option value="cached">Locally cached</option> <option value="history">History</option> </param> <when value="cached"> <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;"> <validator type="unspecified_build" /> <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 --> </param> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;" > <options from_data_table="gatk2_picard_indexes"> <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> </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"> <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;"> <options> <filter type="data_meta" key="dbkey" ref="input_bam" /> </options> </param> </when> </conditional> <conditional name="gatk_param_type"> <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> <option value="basic" selected="True">Basic</option> <option value="advanced">Advanced</option> </param> <when value="basic"> <!-- Do nothing here --> </when> <when value="advanced"> <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"> <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/> </repeat> <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"> <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/> </repeat> <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"> <option value="STRICT" selected="True">STRICT</option> <option value="SILENT">SILENT</option> </param> <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"> <conditional name="read_filter_type"> <param name="read_filter_type_selector" type="select" label="Read Filter Type"> <option value="BadCigar">BadCigar</option> <option value="BadMate">BadMate</option> <option value="DuplicateRead">DuplicateRead</option> <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> <option value="MalformedRead">MalformedRead</option> <option value="MappingQuality">MappingQuality</option> <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> <option value="MappingQualityZero">MappingQualityZero</option> <option value="MateSameStrand">MateSameStrand</option> <option value="MaxInsertSize">MaxInsertSize</option> <option value="MaxReadLength" selected="True">MaxReadLength</option> <option value="MissingReadGroup">MissingReadGroup</option> <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> <option value="Platform454">Platform454</option> <option value="Platform">Platform</option> <option value="PlatformUnit">PlatformUnit</option> <option value="ReadGroupBlackList">ReadGroupBlackList</option> <option value="ReadName">ReadName</option> <option value="ReadStrand">ReadStrand</option> <option value="ReassignMappingQuality">ReassignMappingQuality</option> <option value="Sample">Sample</option> <option value="SingleReadGroup">SingleReadGroup</option> <option value="UnmappedRead">UnmappedRead</option> </param> <when value="BadCigar"> <!-- no extra options --> </when> <when value="BadMate"> <!-- no extra options --> </when> <when value="DuplicateRead"> <!-- no extra options --> </when> <when value="FailsVendorQualityCheck"> <!-- no extra options --> </when> <when value="MalformedRead"> <!-- no extra options --> </when> <when value="MappingQuality"> <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> </when> <when value="MappingQualityUnavailable"> <!-- no extra options --> </when> <when value="MappingQualityZero"> <!-- no extra options --> </when> <when value="MateSameStrand"> <!-- no extra options --> </when> <when value="MaxInsertSize"> <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> </when> <when value="MaxReadLength"> <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> </when> <when value="MissingReadGroup"> <!-- no extra options --> </when> <when value="NoOriginalQualityScores"> <!-- no extra options --> </when> <when value="NotPrimaryAlignment"> <!-- no extra options --> </when> <when value="Platform454"> <!-- no extra options --> </when> <when value="Platform"> <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> </when> <when value="PlatformUnit"> <!-- no extra options --> </when> <when value="ReadGroupBlackList"> <!-- no extra options --> </when> <when value="ReadName"> <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> </when> <when value="ReadStrand"> <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> </when> <when value="ReassignMappingQuality"> <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> </when> <when value="Sample"> <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> </when> <when value="SingleReadGroup"> <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> </when> <when value="UnmappedRead"> <!-- no extra options --> </when> </conditional> </repeat> <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"> <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /> </repeat> <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"> <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /> </repeat> <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"> <option value="UNION" selected="True">UNION</option> <option value="INTERSECTION">INTERSECTION</option> </param> <conditional name="downsampling_type"> <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"> <option value="NONE" selected="True">NONE</option> <option value="ALL_READS">ALL_READS</option> <option value="BY_SAMPLE">BY_SAMPLE</option> </param> <when value="NONE"> <!-- no more options here --> </when> <when value="ALL_READS"> <conditional name="downsample_to_type"> <param name="downsample_to_type_selector" type="select" label="Downsample method"> <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> <option value="downsample_to_coverage">Downsample by Coverage</option> </param> <when value="downsample_to_fraction"> <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/> </when> <when value="downsample_to_coverage"> <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/> </when> </conditional> </when> <when value="BY_SAMPLE"> <conditional name="downsample_to_type"> <param name="downsample_to_type_selector" type="select" label="Downsample method"> <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> <option value="downsample_to_coverage">Downsample by Coverage</option> </param> <when value="downsample_to_fraction"> <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/> </when> <when value="downsample_to_coverage"> <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/> </when> </conditional> </when> </conditional> <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"> <option value="OFF" selected="True">OFF</option> <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option> <option value="RECALCULATE">RECALCULATE</option> </param> <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /> <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"> <option value="STRICT" selected="True">STRICT</option> <option value="LENIENT">LENIENT</option> <option value="SILENT">SILENT</option> <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--> </param> <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"> <option value="ALL" selected="True">ALL</option> <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option> </param> <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"> <conditional name="read_group_black_list_type"> <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> <option value="file" selected="True">Filters in file</option> <option value="text">Specify filters as a string</option> </param> <when value="file"> <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> </when> <when value="text"> <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> </when> </conditional> </repeat> <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/> <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False" help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/> </when> </conditional> <conditional name="analysis_param_type"> <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> <option value="basic" selected="True">Basic</option> <option value="advanced">Advanced</option> </param> <when value="basic"> <!-- Do nothing here --> </when> <when value="advanced"> <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"/> <param name="activeRegionOut" type="boolean" checked="False" truevalue="" falsevalue="" label="activeRegionOut" help="--activeRegionOut / -ARO Output the active region to an interval list file"/> <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="gatk2_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="gatk2_annotations"> <filter type="multiple_splitter" column="tools_valid_for" separator=","/> <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> </options> </param> <param name="comp" type="data" format="vcf" optional="true" label="comp" help="--comp / -comp comparison VCF file"/> <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"> <validator type="in_range" message="value between 0.00 and 1.00" min="0" max="1"/> </param> <param name="dbsnp" type="data" format="vcf" optional="true" label="dbsnp" help="--dbsnp / -D dbSNP file"/> <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"/> <param name="downsampleRegion" type="integer" value="1000" optional="true" label="downsampleRegion" help="--downsampleRegion / -dr coverage, per-sample, to downsample each active region to"/> <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="graphOutput" type="boolean" checked="False" truevalue="" falsevalue="" label="graphOutput" help="--graphOutput / -graph File to which debug assembly graph information should be written"/> <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"/> <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"> <validator type="in_range" message="value between 0 and 127" min="0" max="127"/> </param> <param name="output_mode" type="select" optional="true" label="output_mode" help="--output_mode / -out_mode Specifies which type of calls we should output"> <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="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"> <option value="EXACT">EXACT</option> <option value="ORIGINAL">ORIGINAL</option> <option value="CACHING">CACHING</option> <option value="LOGLESS_CACHING" selected="True">LOGLESS_CACHING</option> </param> <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"/> <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)"/> <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"/> <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"/> <param name="gcpHMM" type="integer" value="10" optional="true" label="gcpHMM" help="--gcpHMM / -gcpHMM Flat gap continuation penalty for use in the Pair HMM"/> <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"/> <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"/> <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"> <option value="EXACT_INDEPENDENT" selected="True">EXACT_INDEPENDENT experimental implementation - for testing only</option> <option value="EXACT_REFERENCE">EXACT_REFERENCE reference implementation of multi-allelic EXACT model. Extremely slow for many alternate alleles</option> <option value="EXACT_ORIGINAL">EXACT_ORIGINAL original biallelic exact model, for testing only</option> <option value="EXACT_GENERAL_PLOIDY">implementation that supports any sample ploidy</option> </param> </when> </conditional> </inputs> <outputs> <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" /> <data format="vcf" name="graph_out" label="${tool.name} on ${on_string} graph" > <filter>analysis_param_type['analysis_param_type_selector'] == "advanced" and analysis_param_type['graphOutput'] == True</filter> </data> <data format="vcf" name="active_region_out" label="${tool.name} on ${on_string} activeRegion" > <filter>analysis_param_type['analysis_param_type_selector'] == "advanced" and analysis_param_type['activeRegionOut'] == True</filter> </data> <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> </outputs> <tests> <test> <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" /> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="phiX.fasta" ftype="fasta" /> <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" /> <param name="gatk_param_type_selector" value="basic" /> <param name="analysis_param_type_selector" value="basic" /> <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" lines_diff="4" /> <output name="output_log" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains" compare="contains" /> </test> </tests> <help> **What it does** **HaplotypeCaller** calls SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region. Haplotypes are evaluated using an affine gap penalty Pair HMM. 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>`_. To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. ------ **Inputs** GenomeAnalysisTK: PrintReads accepts aligned BAM files. **Outputs** The output is a VCF file with raw, unrecalibrated SNP and indel calls. Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. ------- **Settings**:: activeRegionIn Use this interval list file as the active regions to process activeRegionOut Output the active region to this interval list file alleles The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES annotation One or more specific annotations to apply to variant calls comp comparison VCF file contamination Fraction of contamination in sequencing data (for all samples) to aggressively remove dbsnp dbSNP file debug If specified, print out very verbose debug information about each triggering active region downsampleRegion coverage, per-sample, to downsample each active region to excludeAnnotation One or more specific annotations to exclude genotyping_mode Specifies how to determine the alternate alleles to use for genotyping graphOutput File to which debug assembly graph information should be written group One or more classes/groups of annotations to apply to variant calls heterozygosity Heterozygosity value used to compute prior likelihoods for any locus minPruning The minimum allowed pruning factor in assembly graph. Paths with less than or equal supporting kmers are pruned from the graph output_mode Specifies which type of calls we should output pair_hmm_implementation The PairHMM implementation to use for genotype likelihood calculations stand_call_conf The minimum phred-scaled confidence threshold at which variants should be called 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) useAllelesTrigger If specified, use additional trigger on variants found in an external alleles file fullHaplotype If specified, output the full haplotype sequence instead of converting to individual variants w.r.t. the reference gcpHMM Flat gap continuation penalty for use in the Pair HMM genotypeFullActiveRegion If specified, alternate alleles are considered to be the full active region for the purposes of genotyping max_alternate_alleles Maximum number of alternate alleles to genotype p_nonref_model Non-reference probability calculation model to employ ------ **Citation** For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_ Please also site `McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303. Epub 2010 Jul 19. <http://www.ncbi.nlm.nih.gov/pubmed/20644199>`_ If you use this tool in Galaxy, please cite `Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. <http://www.ncbi.nlm.nih.gov/pubmed/20069535>`_ </help> </tool>