Mercurial > repos > iuc > gatk4_mutect2
changeset 0:f41a1e03538b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
| author | iuc |
|---|---|
| date | Wed, 30 Oct 2019 15:33:59 -0400 |
| parents | |
| children | fd2d6e035c3f |
| files | gatk4_Mutect2.xml macros.xml test-data/Mutect2-in1.bam test-data/Mutect2-in2.bam test-data/Mutect2-in2.dict test-data/Mutect2-in3.bam test-data/Mutect2-in4.bam test-data/Mutect2-in5.bam test-data/Mutect2-out1.vcf test-data/Mutect2-out2.vcf test-data/Mutect2-out3.vcf test-data/Mutect2-out4.vcf test-data/Mutect2-out5-1.tabular test-data/Mutect2-out5-2.tabular test-data/Mutect2-out5.bam test-data/Mutect2-out5.vcf test-data/reference.fa tool-data/all_fasta.loc.sample tool-data/tool_data_table_conf.xml.sample |
| diffstat | 19 files changed, 11697 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gatk4_Mutect2.xml Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,758 @@ +<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@0" profile="18.05"> + <description>- Call somatic SNVs and indels via local assembly of haplotypes</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_cmd"/> + <command detect_errors="exit_code"> + <![CDATA[ + #include source=$set_sections# + #include source=$pre_gatk_excl_ints_chth# + #include source=$bam_index_pre_chth# + #include source=$pre_gatk_ints_chth# + + #set ref_flag='--reference="reference.fa"' + + #if str($reference_source.reference_source_selector) == 'history' + ln -s '$reference_source.reference_sequence' reference.fa && + samtools faidx reference.fa && + gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" && + #else if str($reference_source.reference_source_selector) == 'history' + ln -s '$reference_source.reference_sequence.fields.path' reference.fa && + samtools faidx reference.fa && + gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" && + #else + #set ref_flag='' + #end if + + #if str($outputs.output_parameters) == 'yes' + #if str($outputs.debug_activity) == 'yes' + ln -s '$activity_profile_out' activity-profile.tab && + #end if + #if str($outputs.debug_assembly) == 'yes' + ln -s '$assembly_region_out' assembly-region.tab && + #end if + #if str($outputs.debug_bam) == 'yes' + ln -s '$bam_output' debug.bam && + #end if + #end if + + @CMD_BEGIN@ GetSampleName --input="input.bam" --output="samplename.txt" && + sample=`cat samplename.txt` && + + #if str($optional.optional_parameters) == 'yes' + #if $optional.panel_of_normals + #set datatype = $optional.panel_of_normals.datatype + #if $optional.panel_of_normals.is_of_type("vcf_bgzip") + ln -s '$optional.panel_of_normals' panel_of_normals.vcf.gz && + tabix panel_of_normals.vcf.gz && + #else + ln -s '$optional.panel_of_normals' panel_of_normals.vcf && + #end if + #end if + + #if $optional.germline_resource + #set datatype = $optional.germline_resource.datatype + #if $optional.germline_resource.is_of_type("vcf_bgzip") + ln -s '$optional.germline_resource' germline_resource.vcf.gz && + tabix germline_resource.vcf.gz && + #else + ln -s '$optional.germline_resource' germline_resource.vcf && + #end if + #end if + + #if $optional.population_callset + #set datatype = $optional.population_callset.datatype + #if $optional.population_callset.is_of_type("vcf_bgzip") + ln -s '$optional.population_callset' population_callset.vcf.gz && + tabix population_callset.vcf.gz && + #else + ln -s '$optional.population_callset' population_callset.vcf && + #end if + #end if + + #if $optional.alleles + #set datatype = $optional.alleles.datatype + #if $optional.alleles.is_of_type("vcf_bgzip") + ln -s '$optional.alleles' alleles.vcf.gz && + tabix alleles.vcf.gz && + @CMD_BEGIN@ IndexFeatureFile --feature-file alleles.vcf.gz && + #else + ln -s '$optional.alleles' alleles.vcf && + @CMD_BEGIN@ IndexFeatureFile --feature-file alleles.vcf && + #end if + #end if + + #end if + + @CMD_BEGIN@ Mutect2 --QUIET $ref_flag --tumor-sample \$sample + + #include source=$gatk_bam_input# + + ## COMMON PARAMETERS ## + + #if str($common.common_parameters) == 'yes' + + #if $common.read_filter + #for $filter in str($common.read_filter).split(',') + --read-filter="$filter" + #end for + #end if + + #if $common.disable_read_filter + #for $filter in str($common.disable_read_filter).split(',') + --disable-read-filter="$filter" + #end for + #end if + + --verbosity="ERROR" + --read-validation-stringency="$common.read_validation_stringency" + --interval-set-rule="$common.interval_set_rule" + $common.lenient + $common.disable_tool_default_read_filters + $common.add_output_sam_program_record + $common.add_output_vcf_command_line + + #end if + + ## END COMMON PARAMETERS ## + + ## OPTIONAL PARAMETERS ## + + #if str($optional.optional_parameters) == 'yes' + + #if $optional.panel_of_normals + #if $optional.panel_of_normals.is_of_type("vcf_bgzip") + --panel-of-normals panel_of_normals.vcf.gz + #else + --panel-of-normals panel_of_normals.vcf + #end if + #end if + + #if $optional.pedigree + --pedigree="$optional.pedigree" + #end if + + #if $optional.germline_resource + #if $optional.germline_resource.is_of_type("vcf_bgzip") + --germline-resource germline_resource.vcf.gz + #else + --germline-resource germline_resource.vcf + #end if + #end if + + #if $optional.annotation + #for $annot in str($optional.annotation).split(',') + --annotation="$annot" + #end for + #end if + + #if $optional.annotation_group + #for $annot in str($optional.annotation_group).split(',') + --annotation-group="$annot" + #end for + #end if + + #if $optional.annotations_to_exclude + #for $annot in str($optional.annotations_to_exclude).split(',') + --annotations-to-exclude="$annot" + #end for + #end if + + #if $optional.founder_id + --founder-id="$optional.founder_id" + #end if + + #if $optional.normal_sample + --normal-sample="$optional.normal_sample" + #end if + + #if $optional.alleles + --alleles alleles.vcf + #end if + + --base-quality-score-threshold="$optional.base_quality_score_threshold" + --af-of-alleles-not-in-resource="$optional.af_of_alleles_not_in_resource" + --downsampling-stride="$optional.downsampling_stride" + --gcs-max-retries="$optional.gcs_max_retries" + --initial-tumor-lod="$optional.initial_tumor_lod" + --interval-merging-rule="$optional.interval_merging_rule" + --max-population-af="$optional.max_population_af" + --max-reads-per-alignment-start="$optional.max_reads_per_alignment_start" + --min-base-quality-score="$optional.min_base_quality_score" + --native-pair-hmm-threads="\${GALAXY_SLOTS:-1}" + --normal-lod="$optional.normal_lod" + --tumor-lod-to-emit="$optional.tumor_lod_to_emit" + $optional.annotate_with_num_discovered_alleles + $optional.disable_bam_index_caching + $optional.disable_sequence_dictionary_validation + $optional.genotype_germline_sites + $optional.genotype_pon_sites + $optional.native_pair_hmm_use_double_precision + $optional.sites_only_vcf_output + $optional.use_new_qual_calculator + #end if + + ## END OPTIONAL PARAMETERS ## + + ## ADVANCED PARAMETERS ## + + #if str($advanced.advanced_parameters) == 'yes' + + #if $advanced.input_prior + --input-prior="$advanced.input_prior" + #end if + + #if $advanced.kmer_size + --kmer-size="$advanced.kmer_size" + #end if + + --active-probability-threshold="$advanced.active_probability_threshold" + --assembly-region-padding="$advanced.assembly_region_padding" + --bam-writer-type="$advanced.bam_writer_type" + --max-assembly-region-size="$advanced.max_assembly_region_size" + --max-mnp-distance="$advanced.max_mnp_distance" + --max-num-haplotypes-in-population="$advanced.max_num_haplotypes_in_population" + --max-prob-propagation-distance="$advanced.max_prob_propagation_distance" + --max-suspicious-reads-per-alignment-start="$advanced.max_suspicious_reads_per_alignment_start" + --min-assembly-region-size="$advanced.min_assembly_region_size" + --min-dangling-branch-length="$advanced.min_dangling_branch_length" + --min-pruning="$advanced.min_pruning" + --num-pruning-samples="$advanced.num_pruning_samples" + --pair-hmm-gap-continuation-penalty="$advanced.pair_hmm_gap_continuation_penalty" + --pair-hmm-implementation="$advanced.pair_hmm_implementation" + --pcr-indel-model="$advanced.pcr_indel_model" + --phred-scaled-global-read-mismapping-rate="$advanced.phred_scaled_global_read_mismapping_rate" + --smith-waterman="$advanced.smith_waterman" + $advanced.all_site_pls + $advanced.allow_non_unique_kmers_in_ref + $advanced.consensus + $advanced.disable_tool_default_annotations + $advanced.do_not_run_physical_phasing + $advanced.dont_increase_kmer_sizes_for_cycles + $advanced.dont_trim_active_regions + $advanced.dont_use_soft_clipped_bases + $advanced.enable_all_annotations + $advanced.genotype_filtered_alleles + $advanced.use_filtered_reads_for_annotations + + #end if + + ## END ADVANCED PARAMETERS ## + + ## ADDITIONAL OUTPUT PARAMETERS ## + + #if str($outputs.output_parameters) == 'yes' + #if str($outputs.debug_activity) == 'yes' + --activity-profile-out="activity-profile.tab" + #end if + #if str($outputs.debug_assembly) == 'yes' + --assembly-region-out="assembly-region.tab" + #end if + #if str($outputs.debug_bam) == 'yes' + --bam-output="debug.bam" + #end if + #end if + + #include source=$gatk_excl_ints_chth# + #include source=$gatk_ints_chth# + #include source=$vcf_output_opts# + #include source=$gatk_seqdict# + ]]> + </command> + <inputs> + <expand macro="gatk_bam_req_params"/> + <expand macro="gzip_vcf_params"/> + <expand macro="ref_sel"/> + <conditional name="common"> + <param name="common_parameters" type="select" label="Common parameters"> + <option value="no">Use internal defaults</option> + <option value="yes">Specify parameters</option> + </param> + <when value="yes"> + <expand macro="gatk_excl_ints"/> + <expand macro="seq_dict_sel"/> + <param name="add_output_sam_program_record" argument="--add-output-sam-program-record" type="boolean" truevalue="--add-output-sam-program-record" falsevalue="" optional="true" checked="true" label="Add Output Sam Program Record" help="If true, adds a PG tag to created SAM/BAM/CRAM files."/> + <param name="add_output_vcf_command_line" argument="--add-output-vcf-command-line" type="boolean" truevalue="--add-output-vcf-command-line" falsevalue="" optional="true" checked="true" label="Add Output Vcf Command Line" help="If true, adds a command line header line to created VCF files."/> + <param name="disable_read_filter" argument="--disable-read-filter" type="select" multiple="true" value="" label="Disable Read Filter" help="Read filters to be disabled before analysis"> + <option value="GoodCigarReadFilter">Good cigar string</option> + <option value="MappedReadFilter">Mapped read</option> + <option value="MappingQualityAvailableReadFilter">Mapping quality available</option> + <option value="MappingQualityNotZeroReadFilter">Mapping quality not zero</option> + <option value="NonChimericOriginalAlignmentReadFilter">Non-chimeric original alignment</option> + <option value="NonZeroReferenceLengthAlignmentReadFilter">Non-zero reference length alignment</option> + <option value="NotDuplicateReadFilter">Not a duplicate read</option> + <option value="NotSecondaryAlignmentReadFilter">Not a secondary alignment</option> + <option value="PassesVendorQualityCheckReadFilter">Passes vendor quality check</option> + <option value="WellformedReadFilter">Well-formed read</option> + </param> + <param name="disable_tool_default_read_filters" argument="--disable-tool-default-read-filters" type="boolean" truevalue="--disable-tool-default-read-filters" falsevalue="" optional="true" checked="false" label="Disable Tool Default Read Filters" help="Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)"/> + <param name="interval_set_rule" argument="--interval-set-rule" type="select" optional="true" label="Interval Set Rule" help="Set merging approach to use for combining interval inputs"> + <option selected="true" value="UNION">Union</option> + <option value="INTERSECTION">Intersection</option> + </param> + <param name="lenient" argument="--lenient" type="boolean" truevalue="--lenient" falsevalue="" optional="true" checked="false" label="Lenient" help="Lenient processing of VCF files"/> + <param name="read_filter" argument="--read-filter" type="select" multiple="true" value="" label="Read Filter" help="Read filters to be applied before analysis"> + <option value="AlignmentAgreesWithHeaderReadFilter">Alignment agrees with header</option> + <option value="AllowAllReadsReadFilter">Allow all reads</option> + <option value="AmbiguousBaseReadFilter">Ambiguous base</option> + <option value="CigarContainsNoNOperator">Cigar contains no NO operator</option> + <option value="FirstOfPairReadFilter">First of pair</option> + <option value="GoodCigarReadFilter">Good cigar string</option> + <option value="HasReadGroupReadFilter">Has read group</option> + <option value="MappedReadFilter">Mapped read</option> + <option value="MappingQualityAvailableReadFilter">Mapping quality available</option> + <option value="MappingQualityNotZeroReadFilter">Mapping quality not zero</option> + <option value="MatchingBasesAndQualsReadFilter">Matching bases and quals</option> + <option value="MateDifferentStrandReadFilter">Mate different strand</option> + <option value="MateOnSameContigOrNoMappedMateReadFilter">Mate on same contig or no mapped mate</option> + <option value="MateUnmappedAndUnmappedReadFilter">Mate unmapped and mapped</option> + <option value="MetricsReadFilter">Metrics</option> + <option value="NonChimericOriginalAlignmentReadFilter">Non-chimeric original alignment</option> + <option value="NonZeroFragmentLengthReadFilter">Non-zero fragment length</option> + <option value="NonZeroReferenceLengthAlignmentReadFilter">Non-zero reference length alignment</option> + <option value="NotDuplicateReadFilter">Not duplicate</option> + <option value="NotOpticalDuplicateReadFilter">Not optical duplicate</option> + <option value="NotSecondaryAlignmentReadFilter">Not a secondary alignment</option> + <option value="NotSupplementaryAlignmentReadFilter">Not a supplementary alignment</option> + <option value="OverclippedReadFilter">Overclipped</option> + <option value="PairedReadFilter">Paired</option> + <option value="PassesVendorQualityCheckReadFilter">Passes vendor quality check</option> + <option value="PrimaryLineReadFilter">Primary line</option> + <option value="ProperlyPairedReadFilter">Properly paired</option> + <option value="ReadLengthEqualsCigarLengthReadFilter">Read length equals cigar length</option> + <option value="SecondOfPairReadFilter">Second of pair</option> + <option value="SeqIsStoredReadFilter">Sequence is stored</option> + <option value="SoftClippedReadFilter">Soft clipped</option> + <option value="ValidAlignmentStartReadFilter">Valid alignment start</option> + <option value="ValidAlignmentEndReadFilter">Valid alignment end</option> + <option value="WellformedReadFilter">Well-formed read</option> + </param> + <param name="read_validation_stringency" argument="--read-validation-stringency" type="select" optional="true" label="Read Validation Stringency" help="Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded."> + <option selected="true" value="SILENT">Silent</option> + <option value="STRICT">Strict</option> + <option value="LENIENT">Lenient</option> + </param> + </when> + <when value="no" /> + </conditional> + <conditional name="optional"> + <param name="optional_parameters" type="select" label="Optional parameters"> + <option value="no">Use internal defaults</option> + <option value="yes">Specify parameters</option> + </param> + <when value="yes"> + <expand macro="gatk_ints"/> + <param name="af_of_alleles_not_in_resource" argument="--af-of-alleles-not-in-resource" type="float" optional="true" value="-1.0" label="Af Of Alleles Not In Resource" help="Population allele fraction assigned to alleles not found in germline resource. Please see docs/mutect/mutect2.pdf fora derivation of the default value."/> + <param name="annotate_with_num_discovered_alleles" argument="--annotate-with-num-discovered-alleles" type="boolean" truevalue="--annotate-with-num-discovered-alleles" falsevalue="" optional="true" checked="false" label="Annotate With Num Discovered Alleles" help="If provided, we will annotate records with the number of alternate alleles that were discovered (but not necessarily genotyped) at a given site"/> + <param argument="--annotation" type="select" multiple="true" label="Annotations" help="One or more specific annotations to add to variant calls"> + <option value="AlleleFraction">AlleleFraction</option> + <option value="AS_BaseQualityRankSumTest">AS_BaseQualityRankSumTest</option> + <option value="AS_FisherStrand">AS_FisherStrand</option> + <option value="AS_InbreedingCoeff">AS_InbreedingCoeff</option> + <option value="AS_MappingQualityRankSumTest">AS_MappingQualityRankSumTest</option> + <option value="AS_QualByDepth">AS_QualByDepth</option> + <option value="AS_ReadPosRankSumTest">AS_ReadPosRankSumTest</option> + <option value="AS_RMSMappingQuality">AS_RMSMappingQuality</option> + <option value="AS_StrandOddsRatio">AS_StrandOddsRatio</option> + <option value="BaseQuality">BaseQuality</option> + <option value="BaseQualityHistogram">BaseQualityHistogram</option> + <option value="BaseQualityRankSumTest">BaseQualityRankSumTest</option> + <option value="ChromosomeCounts">ChromosomeCounts</option> + <option value="ClippingRankSumTest">ClippingRankSumTest</option> + <option value="CountNs">CountNs</option> + <option value="Coverage">Coverage</option> + <option value="DepthPerAlleleBySample">DepthPerAlleleBySample</option> + <option value="DepthPerSampleHC">DepthPerSampleHC</option> + <option value="ExcessHet">ExcessHet</option> + <option value="FisherStrand">FisherStrand</option> + <option value="FragmentLength">FragmentLength</option> + <option value="GenotypeSummaries">GenotypeSummaries</option> + <option value="InbreedingCoeff">InbreedingCoeff</option> + <option value="LikelihoodRankSumTest">LikelihoodRankSumTest</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityRankSumTest">MappingQualityRankSumTest</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="OrientationBiasReadCounts">OrientationBiasReadCounts</option> + <option value="OriginalAlignment">OriginalAlignment</option> + <option value="PossibleDeNovo">PossibleDeNovo</option> + <option value="QualByDepth">QualByDepth</option> + <option value="ReadPosition">ReadPosition</option> + <option value="ReadPosRankSumTest">ReadPosRankSumTest</option> + <option value="ReferenceBases">ReferenceBases</option> + <option value="RMSMappingQuality">RMSMappingQuality</option> + <option value="SampleList">SampleList</option> + <option value="StrandBiasBySample">StrandBiasBySample</option> + <option value="StrandOddsRatio">StrandOddsRatio</option> + <option value="TandemRepeat">TandemRepeat</option> + <option value="UniqueAltReadCount">UniqueAltReadCount</option> + </param> + <param name="annotation_group" argument="--annotation-group" type="select" multiple="true" label="Annotation groups" help="One or more annotation groups to add to variant calls"> + <option value="AlleleSpecificAnnotation">AlleleSpecificAnnotation</option> + <option value="AS_StandardAnnotation">AS_StandardAnnotation</option> + <option value="ReducibleAnnotation">ReducibleAnnotation</option> + <option value="StandardAnnotation">StandardAnnotation</option> + <option value="StandardHCAnnotation">StandardHCAnnotation</option> + <option value="StandardMutectAnnotation">StandardMutectAnnotation</option> + </param> + <param name="annotations_to_exclude" argument="--annotations-to-exclude" type="select" multiple="true" label="Annotations to exclude" help="Specific annotations to exclude from variant calls"> + <option value="AlleleFraction">AlleleFraction</option> + <option value="AS_BaseQualityRankSumTest">AS_BaseQualityRankSumTest</option> + <option value="AS_FisherStrand">AS_FisherStrand</option> + <option value="AS_InbreedingCoeff">AS_InbreedingCoeff</option> + <option value="AS_MappingQualityRankSumTest">AS_MappingQualityRankSumTest</option> + <option value="AS_QualByDepth">AS_QualByDepth</option> + <option value="AS_ReadPosRankSumTest">AS_ReadPosRankSumTest</option> + <option value="AS_RMSMappingQuality">AS_RMSMappingQuality</option> + <option value="AS_StrandOddsRatio">AS_StrandOddsRatio</option> + <option value="BaseQuality">BaseQuality</option> + <option value="BaseQualityHistogram">BaseQualityHistogram</option> + <option value="BaseQualityRankSumTest">BaseQualityRankSumTest</option> + <option value="ChromosomeCounts">ChromosomeCounts</option> + <option value="ClippingRankSumTest">ClippingRankSumTest</option> + <option value="CountNs">CountNs</option> + <option value="Coverage">Coverage</option> + <option value="DepthPerAlleleBySample">DepthPerAlleleBySample</option> + <option value="DepthPerSampleHC">DepthPerSampleHC</option> + <option value="ExcessHet">ExcessHet</option> + <option value="FisherStrand">FisherStrand</option> + <option value="FragmentLength">FragmentLength</option> + <option value="GenotypeSummaries">GenotypeSummaries</option> + <option value="InbreedingCoeff">InbreedingCoeff</option> + <option value="LikelihoodRankSumTest">LikelihoodRankSumTest</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityRankSumTest">MappingQualityRankSumTest</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="OrientationBiasReadCounts">OrientationBiasReadCounts</option> + <option value="OriginalAlignment">OriginalAlignment</option> + <option value="PossibleDeNovo">PossibleDeNovo</option> + <option value="QualByDepth">QualByDepth</option> + <option value="ReadPosition">ReadPosition</option> + <option value="ReadPosRankSumTest">ReadPosRankSumTest</option> + <option value="ReferenceBases">ReferenceBases</option> + <option value="RMSMappingQuality">RMSMappingQuality</option> + <option value="SampleList">SampleList</option> + <option value="StrandBiasBySample">StrandBiasBySample</option> + <option value="StrandOddsRatio">StrandOddsRatio</option> + <option value="TandemRepeat">TandemRepeat</option> + <option value="UniqueAltReadCount">UniqueAltReadCount</option> + </param> + <param name="pedigree" argument="--pedigree" type="data" optional="true" format="vcf,vcf_bgzip" label="Pedigree" help="Pedigree file for determining the population "founders". If a file is provided here, a pedigree-based annotation must be added above."/> + <param name="base_quality_score_threshold" argument="--base-quality-score-threshold" type="integer" optional="true" value="18" label="Base Quality Score Threshold" help="Base qualities below this threshold will be reduced to the minimum (6)"/> + <param name="contamination_fraction_to_filter" argument="--contamination-fraction-to-filter" type="float" optional="true" value="0.0" label="Contamination Fraction To Filter" help="Fraction of contamination in sequencing data (for all samples) to aggressively remove"/> + <param name="disable_bam_index_caching" argument="--disable-bam-index-caching" type="boolean" truevalue="--disable-bam-index-caching" falsevalue="" optional="true" checked="false" label="Disable Bam Index Caching" help="If true, don&apos;t cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified."/> + <param name="disable_sequence_dictionary_validation" argument="--disable-sequence-dictionary-validation" type="boolean" truevalue="--disable-sequence-dictionary-validation" falsevalue="" optional="true" checked="false" label="Disable Sequence Dictionary Validation" help="If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!"/> + <param name="downsampling_stride" argument="--downsampling-stride" type="integer" optional="true" value="1" label="Downsampling Stride" help="Downsample a pool of reads starting within a range of one or more bases."/> + <param name="founder_id" argument="--founder-id" type="text" optional="true" value="" label="Founder Id" help="Samples representing the population &quot;founders&quot;"/> + <param name="gcs_max_retries" argument="--gcs-max-retries" type="integer" optional="true" value="20" label="Gcs Max Retries" help="If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection"/> + <param name="genotype_germline_sites" argument="--genotype-germline-sites" type="boolean" truevalue="--genotype-germline-sites" falsevalue="" optional="true" checked="false" label="Genotype Germline Sites" help="(EXPERIMENTAL) Call all apparent germline site even though they will ultimately be filtered."/> + <param name="genotype_pon_sites" argument="--genotype-pon-sites" type="boolean" truevalue="--genotype-pon-sites" falsevalue="" optional="true" checked="false" label="Genotype PoN Sites" help="Call sites in the PoN even though they will ultimately be filtered."/> + <param name="alleles" argument="--alleles" type="data" optional="true" format="vcf" label="Alleles" help="The set of alleles at which to genotype"/> + <param name="germline_resource" argument="--germline-resource" type="data" optional="true" format="vcf,vcf_bgzip" label="Germline Resource" help="Population vcf of germline sequencing containing allele fractions."/> + <param name="heterozygosity" argument="--heterozygosity" type="float" optional="true" value="0.001" label="Heterozygosity" help="The expected heterozygosity value used to compute prior probability that a locus is non-reference. The default priors are for provided for humans: het = 1e-3 which means that the probability of N samples being hom-ref at a site is: 1 - sum_i_2N (het / i) Note that heterozygosity as used here is the population genetics concept: http://en.wikipedia.org/wiki/Zygosity#Heterozygosity_in_population_genetics That is, a hets value of 0.01 implies that two randomly chosen chromosomes from the population of organisms would differ from each other (one being A and the other B) at a rate of 1 in 100 bp. Note that this quantity has nothing to do with the likelihood of any given sample having a heterozygous genotype, which in the GATK is purely determined by the probability of the observed data P(D | AB) under the model that there may be a AB het genotype. The posterior probability of this AB genotype would use the het prior, but the GATK only uses this posterior probability in determining the prob. that a site is polymorphic. So changing the het parameters only increases the chance that a site will be called non-reference across all samples, but doesn't actually change the output genotype likelihoods at all, as these aren't posterior probabilities at all. The quantity that changes whether the GATK considers the possibility of a het genotype at all is the ploidy, which determines how many chromosomes each individual in the species carries."/> + <param name="heterozygosity_stdev" argument="--heterozygosity-stdev" type="float" optional="true" value="0.01" label="Heterozygosity Stdev" help="Standard deviation of heterozygosity for SNP and indel calling."/> + <param name="indel_heterozygosity" argument="--indel-heterozygosity" type="float" optional="true" value="0.000125" label="Indel Heterozygosity" help="Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on the meaning of this population genetics concept"/> + <param name="initial_tumor_lod" argument="--initial-tumor-lod" type="float" optional="true" value="2.0" label="Initial Tumor Lod" help="LOD threshold to consider pileup active."/> + <param name="interval_merging_rule" argument="--interval-merging-rule" type="select" optional="true" label="Interval Merging Rule" help="Interval merging rule for abutting intervals"> + <option selected="true" value="ALL">All</option> + <option value="OVERLAPPING_ONLY">Overlapping only</option> + </param> + <param name="max_population_af" argument="--max-population-af" type="float" optional="true" value="0.01" label="Max Population Af" help="Maximum population allele frequency in tumor-only mode."/> + <param name="max_reads_per_alignment_start" argument="--max-reads-per-alignment-start" type="integer" optional="true" value="50" label="Max Reads Per Alignment Start" help="Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable."/> + <param name="min_base_quality_score" argument="--min-base-quality-score" type="integer" optional="true" value="10" label="Min Base Quality Score" help="Minimum base quality required to consider a base for calling"/> + <param name="native_pair_hmm_use_double_precision" argument="--native-pair-hmm-use-double-precision" type="boolean" truevalue="--native-pair-hmm-use-double-precision" falsevalue="" optional="true" checked="false" label="Native Pair Hmm Use Double Precision" help="use double precision in the native pairHmm. This is slower but matches the java implementation better"/> + <param name="normal_lod" argument="--normal-lod" type="float" optional="true" value="2.2" label="Normal Lod" help="LOD threshold for calling normal variant non-germline."/> + <param name="normal_sample" argument="--normal-sample" type="text" optional="true" value="" label="Normal Sample" help="BAM sample name of normal. May be URL-encoded as output by GetSampleName with -encode argument."/> + <param name="num_reference_samples_if_no_call" argument="--num-reference-samples-if-no-call" type="integer" optional="true" value="0" label="Num Reference Samples If No Call" help="Number of hom-ref genotypes to infer at sites not present in a panel"/> + <param name="output_mode" argument="--output-mode" type="select" optional="true" label="Output Mode" help="Specifies which type of calls we should output"> + <option selected="true" value="EMIT_VARIANTS_ONLY">Variants only</option> + <option value="EMIT_ALL_CONFIDENT_SITES">All confident sites</option> + <option value="EMIT_ALL_SITES">All sites</option> + </param> + <param name="panel_of_normals" argument="--panel-of-normals" type="data" optional="true" format="vcf,vcf_bgzip" label="Panel Of Normals" help="VCF file of sites observed in normal."/> + <param name="sites_only_vcf_output" argument="--sites-only-vcf-output" type="boolean" truevalue="--sites-only-vcf-output" falsevalue="" optional="true" checked="false" label="Sites Only Vcf Output" help="If true, don't emit genotype fields when writing vcf file output."/> + <param name="population_callset" argument="--population-callset" type="data" optional="true" format="" label="Population Callset" help="Callset to use in calculating genotype priors"/> + <param name="sample_ploidy" argument="--sample-ploidy" type="integer" optional="true" value="2" label="Sample Ploidy" help="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)."/> + <param name="sites_only_vcf_output" argument="--sites-only-vcf-output" type="boolean" truevalue="--sites-only-vcf-output" falsevalue="" optional="true" checked="false" label="Sites Only Vcf Output" help="If true, don&apos;t emit genotype fields when writing vcf file output."/> + <param name="standard_min_confidence_threshold_for_calling" argument="--standard-min-confidence-threshold-for-calling" type="float" optional="true" value="10.0" label="Standard Min Confidence Threshold For Calling" help="The minimum phred-scaled confidence threshold at which variants should be called"/> + <param name="tumor_lod_to_emit" argument="--tumor-lod-to-emit" type="float" optional="true" value="3.0" label="Tumor Lod To Emit" help="LOD threshold to emit tumor variant to VCF."/> + <param name="use_new_qual_calculator" argument="--use-new-qual-calculator" type="boolean" truevalue="--use-new-qual-calculator" falsevalue="" optional="true" checked="false" label="Use New Qual Calculator" help="If provided, we will use the new AF model instead of the so-called exact model"/> + </when> + <when value="no" /> + </conditional> + <conditional name="advanced"> + <param name="advanced_parameters" type="select" label="Advanced parameters"> + <option value="no">Use internal defaults</option> + <option value="yes">Specify parameters</option> + </param> + <when value="yes"> + <param name="active_probability_threshold" argument="--active-probability-threshold" type="float" optional="true" value="0.002" label="Active Probability Threshold" help="Minimum probability for a locus to be considered active."/> + <param name="all_site_pls" argument="--all-site-pls" type="boolean" truevalue="--all-site-pls" falsevalue="" optional="true" checked="false" label="All Site Pls" help="Annotate all sites with PLs"/> + <param name="allow_non_unique_kmers_in_ref" argument="--allow-non-unique-kmers-in-ref" type="boolean" truevalue="--allow-non-unique-kmers-in-ref" falsevalue="" optional="true" checked="false" label="Allow Non Unique Kmers In Ref" help="Allow graphs that have non-unique kmers in the reference"/> + <param name="assembly_region_padding" argument="--assembly-region-padding" type="integer" optional="true" value="100" label="Assembly Region Padding" help="Number of additional bases of context to include around each assembly region"/> + <param name="bam_writer_type" argument="--bam-writer-type" type="select" optional="true" label="Bam Writer Type" help="Which haplotypes should be written to the BAM"> + <option selected="true" value="CALLED_HAPLOTYPES">Called haplotypes</option> + <option value="ALL_POSSIBLE_HAPLOTYPES">All possible haplotypes</option> + </param> + <param name="consensus" argument="--consensus" type="boolean" truevalue="--consensus" falsevalue="" optional="true" checked="false" label="Consensus" help="1000G consensus mode"/> + <param name="disable_tool_default_annotations" argument="--disable-tool-default-annotations" type="boolean" truevalue="--disable-tool-default-annotations" falsevalue="" optional="true" checked="false" label="Disable Tool Default Annotations" help="Disable all tool default annotations"/> + <param name="do_not_run_physical_phasing" argument="--do-not-run-physical-phasing" type="boolean" truevalue="--do-not-run-physical-phasing" falsevalue="" optional="true" checked="false" label="Do Not Run Physical Phasing" help="Disable physical phasing"/> + <param name="dont_increase_kmer_sizes_for_cycles" argument="--dont-increase-kmer-sizes-for-cycles" type="boolean" truevalue="--dont-increase-kmer-sizes-for-cycles" falsevalue="" optional="true" checked="false" label="Dont Increase Kmer Sizes For Cycles" help="Disable iterating over kmer sizes when graph cycles are detected"/> + <param name="dont_trim_active_regions" argument="--dont-trim-active-regions" type="boolean" truevalue="--dont-trim-active-regions" falsevalue="" optional="true" checked="false" label="Dont Trim Active Regions" help="If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping"/> + <param name="dont_use_soft_clipped_bases" argument="--dont-use-soft-clipped-bases" type="boolean" truevalue="--dont-use-soft-clipped-bases" falsevalue="" optional="true" checked="false" label="Dont Use Soft Clipped Bases" help="Do not analyze soft clipped bases in the reads"/> + <param name="enable_all_annotations" argument="--enable-all-annotations" type="boolean" truevalue="--enable-all-annotations" falsevalue="" optional="true" checked="false" label="Enable All Annotations" help="Use all possible annotations (not for the faint of heart)"/> + <param name="genotype_filtered_alleles" argument="--genotype-filtered-alleles" type="boolean" truevalue="--genotype-filtered-alleles" falsevalue="" optional="true" checked="false" label="Genotype Filtered Alleles" help="Whether to genotype all given alleles, even filtered ones, --genotyping_mode is GENOTYPE_GIVEN_ALLELES"/> + <param name="input_prior" argument="--input-prior" type="float" optional="true" value="" label="Input Prior" help="By default, the prior specified with the heterozygosity argument is used for variant discovery at a particular locus, using an infinite sites model, see e.g. Waterson (1975) or Tajima (1996). This model asserts that the probability of having a population of k variant sites in N chromosomes is proportional to theta/k, for 1=1:N There are instances where using this prior might not be desireable, e.g. for population studies where prior might not be appropriate, as for example when the ancestral status of the reference allele is not known. By using this argument, user can manually specify priors to be used for calling as a vector for doubles, with the following restriciotns: a) User must specify 2N values, where N is the number of samples. b) Only diploid calls supported. c) Probability values are specified in double format, in linear space. d) No negative values allowed. e) Values will be added and Pr(AC=0) will be 1-sum, so that they sum up to one. f) If user-defined values add to more than one, an error will be produced. If user wants completely flat priors, then user should specify the same value (=1/(2*N+1)) 2*N times,e.g. -inputPrior 0.33 -inputPrior 0.33 for the single-sample diploid case."/> + <param name="kmer_size" argument="--kmer-size" type="integer" optional="true" value="" label="Kmer Size" help="Kmer size to use in the read threading assembler"/> + <param name="max_assembly_region_size" argument="--max-assembly-region-size" type="integer" optional="true" value="300" label="Max Assembly Region Size" help="Maximum size of an assembly region"/> + <param name="max_mnp_distance" argument="--max-mnp-distance" type="integer" optional="true" value="1" label="Max Mnp Distance" help="Two or more phased substitutions separated by this distance or less are merged into MNPs."/> + <param name="max_num_haplotypes_in_population" argument="--max-num-haplotypes-in-population" type="integer" optional="true" value="128" label="Max Num Haplotypes In Population" help="Maximum number of haplotypes to consider for your population"/> + <param name="max_prob_propagation_distance" argument="--max-prob-propagation-distance" type="integer" optional="true" value="50" label="Max Prob Propagation Distance" help="Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions"/> + <param name="max_suspicious_reads_per_alignment_start" argument="--max-suspicious-reads-per-alignment-start" type="integer" optional="true" value="0" label="Max Suspicious Reads Per Alignment Start" help="Maximum number of suspicious reads (mediocre mapping quality or too many substitutions) allowed in a downsampling stride. Set to 0 to disable."/> + <param name="min_assembly_region_size" argument="--min-assembly-region-size" type="integer" optional="true" value="50" label="Min Assembly Region Size" help="Minimum size of an assembly region"/> + <param name="min_dangling_branch_length" argument="--min-dangling-branch-length" type="integer" optional="true" value="4" label="Min Dangling Branch Length" help="Minimum length of a dangling branch to attempt recovery"/> + <param name="min_pruning" argument="--min-pruning" type="integer" optional="true" value="2" label="Min Pruning" help="Minimum support to not prune paths in the graph"/> + <param name="num_pruning_samples" argument="--num-pruning-samples" type="integer" optional="true" value="1" label="Num Pruning Samples" help="Number of samples that must pass the minPruning threshold"/> + <param name="pair_hmm_gap_continuation_penalty" argument="--pair-hmm-gap-continuation-penalty" type="integer" optional="true" value="10" label="Pair Hmm Gap Continuation Penalty" help="Flat gap continuation penalty for use in the Pair HMM"/> + <param name="pair_hmm_implementation" argument="--pair-hmm-implementation" type="select" optional="true" label="Pair Hmm Implementation" help="The PairHMM implementation to use for genotype likelihood calculations"> + <option selected="true" value="FASTEST_AVAILABLE">Fastest Available</option> + <option value="EXACT">Exact</option> + <option value="ORIGINAL">Original</option> + <option value="LOGLESS_CACHING">Logless Caching</option> + <option value="AVX_LOGLESS_CACHING">Logless Caching (AVX)</option> + <option value="AVX_LOGLESS_CACHING_OMP">Logless Caching (AVX+OMP)</option> + <option value="EXPERIMENTAL_FPGA_LOGLESS_CACHING">Logless Caching (FPGA, Experimental)</option> + </param> + <param name="pcr_indel_model" argument="--pcr-indel-model" type="select" optional="true" label="Pcr Indel Model" help="The PCR indel model to use"> + <option selected="true" value="CONSERVATIVE">Conservative</option> + <option value="NONE">None</option> + <option value="HOSTILE">Hostile</option> + <option value="AGGRESSIVE">Aggressive</option> + </param> + <param name="phred_scaled_global_read_mismapping_rate" argument="--phred-scaled-global-read-mismapping-rate" type="integer" optional="true" value="45" label="Phred Scaled Global Read Mismapping Rate" help="The global assumed mismapping rate for reads"/> + <param name="smith_waterman" argument="--smith-waterman" type="select" optional="true" label="Smith Waterman" help="Which Smith-Waterman implementation to use, generally 'Fastest available' is the right choice"> + <option selected="true" value="FASTEST_AVAILABLE">Fastest available</option> + <option value="AVX_ENABLED">AVX-Enabled</option> + <option value="JAVA">JAVA</option> + </param> + <param name="use_filtered_reads_for_annotations" argument="--use-filtered-reads-for-annotations" type="boolean" truevalue="--use-filtered-reads-for-annotations" falsevalue="" optional="true" checked="false" label="Use Filtered Reads For Annotations" help="Use the contamination-filtered read maps for the purposes of annotating variants"/> + </when> + <when value="no" /> + </conditional> + <conditional name="outputs"> + <param name="output_parameters" type="select" label="Output parameters" help="Additional outputs for debugging purposes"> + <option value="no">Output only variants</option> + <option value="yes">Generate debugging information</option> + </param> + <when value="yes"> + <param name="debug_activity" argument="--activity-profile-out" type="boolean" checked="false" truevalue="yes" falsevalue="" label="Activity Profile Out" help="Output the raw activity profile results in IGV format"/> + <param name="debug_assembly" argument="--assembly-region-out" type="boolean" checked="false" truevalue="yes" falsevalue="" label="Assembly Region Out" help="Output the assembly region to this IGV formatted file"/> + <param name="debug_bam" argument="--bam-output" type="boolean" checked="false" truevalue="yes" falsevalue="" label="Bam Output" help="The assembled haplotypes and locally realigned reads will be written as BAM to this file if requested. This is intended to be used only for troubleshooting purposes, in specific areas where you want to better understand why the caller is making specific calls"/> + </when> + <when value="no" /> + </conditional> + </inputs> + <outputs> + <expand macro="gzip_vcf_output_params"/> + <data format="tabular" name="activity_profile_out" label="${tool.name} on ${on_string}: Activity profile"> + <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_activity']</filter> + </data> + <data format="tabular" name="assembly_region_out" label="${tool.name} on ${on_string}: Assembly region"> + <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_assembly']</filter> + </data> + <data format="bam" name="bam_output" label="${tool.name} on ${on_string}: Debug BAM output"> + <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_bam']</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" ftype="bam" value="Mutect2-in1.bam" /> + <param name="reference_sequence" ftype="fasta" value="reference.fa" /> + <param name="gzipped_output" value="false" /> + <param name="reference_source_selector" value="history" /> + <param name="common_parameters" value="no" /> + <param name="optional_parameters" value="no" /> + <param name="advanced_parameters" value="no" /> + <param name="output_parameters" value="no" /> + <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="2" /> + </test> + <test> + <param name="input" ftype="bam" value="Mutect2-in2.bam" /> + <param name="reference_sequence" ftype="fasta" value="reference.fa" /> + <param name="gzipped_output" value="false" /> + <param name="reference_source_selector" value="history" /> + <param name="common_parameters" value="yes" /> + <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" /> + <param name="seqdict_source" value="history" /> + <param name="seqdict_sequence" value="Mutect2-in2.dict" /> + <param name="optional_parameters" value="no" /> + <param name="advanced_parameters" value="no" /> + <param name="output_parameters" value="no" /> + <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="2" /> + </test> + <test> + <param name="input" ftype="bam" value="Mutect2-in3.bam" /> + <param name="reference_sequence" ftype="fasta" value="reference.fa" /> + <param name="gzipped_output" value="false" /> + <param name="reference_source_selector" value="history" /> + <param name="common_parameters" value="no" /> + <param name="optional_parameters" value="yes" /> + <param name="annotation" value="StrandBiasBySample,BaseQualityHistogram,OrientationBiasReadCounts" /> + <param name="annotation_group" value="StandardMutectAnnotation" /> + <param name="advanced_parameters" value="no" /> + <param name="output_parameters" value="no" /> + <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="2" /> + </test> + <test> + <param name="input" ftype="bam" value="Mutect2-in4.bam" /> + <param name="reference_sequence" ftype="fasta" value="reference.fa" /> + <param name="gzipped_output" value="false" /> + <param name="reference_source_selector" value="history" /> + <param name="common_parameters" value="no" /> + <param name="optional_parameters" value="yes" /> + <param name="advanced_parameters" value="yes" /> + <param name="dont_trim_active_regions" value="true" /> + <param name="output_parameters" value="no" /> + <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" /> + </test> + <test> + <param name="input" ftype="bam" value="Mutect2-in5.bam" /> + <param name="reference_sequence" ftype="fasta" value="reference.fa" /> + <param name="gzipped_output" value="false" /> + <param name="reference_source_selector" value="history" /> + <param name="common_parameters" value="no" /> + <param name="optional_parameters" value="no" /> + <param name="advanced_parameters" value="no" /> + <param name="output_parameters" value="yes" /> + <param name="debug_activity" value="true" /> + <param name="debug_assembly" value="true" /> + <param name="debug_bam" value="true" /> + <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="2" /> + <output name="activity_profile_out" file="Mutect2-out5-1.tabular" /> + <output name="assembly_region_out" file="Mutect2-out5-2.tabular" /> + <output name="bam_output" file="Mutect2-out5.bam" /> + </test> + </tests> + <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short +variants include single nucleotide (SNV) and insertion and deletion +(indel) variants. The caller combines the DREAM challenge-winning +somatic genotyping engine of the original MuTect (`Cibulskis et al., +2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__) +with the assembly-based machinery of +`HaplotypeCaller <https://www.broadinstitute.org/gatk/documentation/tooldocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php>`__. + +This tool is featured in the *Somatic Short Mutation calling Best +Practice Workflow*. See +`Tutorial#11136 <https://software.broadinstitute.org/gatk/documentation/article?id=11136>`__ +for a step-by-step description of the workflow and +`Article#11127 <https://software.broadinstitute.org/gatk/documentation/article?id=11127>`__ +for an overview of what traditional somatic calling entails. For the +latest pipeline scripts, see the `Mutect2 WDL scripts +directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__. +Although we present the tool for somatic calling, it may apply to other +contexts, such as mitochondrial variant calling. + +Usage examples +~~~~~~~~~~~~~~ + +Example commands show how to run Mutect2 for typical scenarios. The two +modes are (i) *somatic mode* where a tumor sample is matched with a +normal sample in analysis and (ii) *tumor-only mode* where a single +sample's alignment data undergoes analysis. + +(i) Tumor with matched normal +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Given a matched normal, Mutect2 is designed to call somatic variants +only. The tool includes logic to skip emitting variants that are clearly +present in the germline based on provided evidence, e.g. in the matched +normal. This is done at an early stage to avoid spending computational +resources on germline events. If the variant's germline status is +borderline, then Mutect2 will emit the variant to the callset for +subsequent filtering and review. + +:: + + gatk Mutect2 \ + -R reference.fa \ + -I tumor.bam \ + -tumor tumor_sample_name \ + -I normal.bam \ + -normal normal_sample_name \ + --germline-resource af-only-gnomad.vcf.gz \ + --af-of-alleles-not-in-resource 0.00003125 \ + --panel-of-normals pon.vcf.gz \ + -O somatic.vcf.gz + + +The --af-of-alleles-not-in-resource argument value should match +expectations for alleles not found in the provided germline resource. +Note the tool does not require a germline resource nor a panel of +normals (PoN) to run. The tool prefilters sites for the matched normal +and the PoN. For the germline resource, the tool prefilters on the +allele. Below is an excerpt of a known variants resource with population +allele frequencies + +:: + + #CHROM POS ID REF ALT QUAL FILTER INFO + 1 10067 . T TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 30.35 PASS AC=3;AF=7.384E-5 + 1 10108 . CAACCCT C 46514.32 PASS AC=6;AF=1.525E-4 + 1 10109 . AACCCTAACCCT AAACCCT,* 89837.27 PASS AC=48,5;AF=0.001223,1.273E-4 + 1 10114 . TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA *,CAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA,T 36728.97 PASS AC=55,9,1;AF=0.001373,2.246E-4,2.496E-5 + 1 10119 . CT C,* 251.23 PASS AC=5,1;AF=1.249E-4,2.498E-5 + 1 10120 . TA CA,* 14928.74 PASS AC=10,6;AF=2.5E-4,1.5E-4 + 1 10128 . ACCCTAACCCTAACCCTAAC A,* 285.71 PASS AC=3,1;AF=7.58E-5,2.527E-5 + 1 10131 . CT C,* 378.93 PASS AC=7,5;AF=1.765E-4,1.261E-4 + 1 10132 . TAACCC *,T 18025.11 PASS AC=12,2;AF=3.03E-4,5.049E-5 + + +(ii) Tumor-only mode +^^^^^^^^^^^^^^^^^^^^ + +This mode runs on a single sample, e.g. single tumor or single normal +sample. To create a PoN, call on each normal sample in this mode, then +use CreateSomaticPanelOfNormals to generate the PoN. + +:: + + gatk Mutect2 \ + -R reference.fa \ + -I sample.bam \ + -tumor sample_name \ + -O single_sample.vcf.gz + + +Further points of interest +~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Additional parameters that factor towards filtering, including +normal-artifact-lod (default threshold 0.0) and tumor-lod (default +threshold 5.3), are available in FilterMutectCalls. While the tool +calculates normal-lod assuming a diploid genotype, it calculates +normal-artifact-lod with the same approach it uses for tumor-lod, i.e. +with a variable ploidy assumption. + +- If the normal artifact log odds becomes large, then FilterMutectCalls applies the artifact-in-normal filter. For matched normal samples with tumor contamination, consider increasing the normal-artifact-lod threshold. + +- The tumor log odds, which is calculated independently of any matched normal, determines whether to filter a tumor variant. Variants with tumor LODs exceeding the threshold pass filtering. + + +If a variant is absent from a given germline resource, then the value +for --af-of-alleles-not-in-resource applies. For example, gnomAD's +16,000 samples (~32,000 homologs per locus) becomes a probability of one +in 32,000 or less. Thus, an allele's absence from the germline resource +becomes evidence that it is not a germline variant. + +Caveats +~~~~~~~ + +Although GATK4 Mutect2 accomodates varying coverage depths, further +optimization of parameters may improve calling for extreme high depths, +e.g. 1000X. +]]></help> + <citations> + <expand macro="citations"/> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,710 @@ +<?xml version="1.0"?> +<macros> + <token name="@VERSION@">4.1.4.0</token> + <token name="@WRAPPER_VERSION@">@VERSION@+galaxy</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">gatk4</requirement> + <requirement type="package" version="0.2.5">tabix</requirement> + <requirement type="package" version="1.9">samtools</requirement> + <yield /> + </requirements> + </xml> + + <!--Hacky way to determine GATK version, for display in tool info--> + <xml name="version_cmd"> + <version_command>gatk SortSam --version 2>&1 | grep Version | cut -d ':' -f 2</version_command> + </xml> + + <!--Command token, java options should not be hard coded here.--> + <token name="@CMD_BEGIN@">[[ -z \$_JAVA_OPTIONS ]] && export JAVA_OPTS=\$_JAVA_OPTIONS && gatk</token> + + <!--Define sections that parameters could exist within.--> + <template name="set_sections"> + #set global $sections = ['', 'optional.', 'advanced.', 'common.', 'deprecated.'] + </template> + + <!--Reference genome handling--> + <!--One template each for the different reference genome parameter names.--> + <!--TODO: Can the reference parameters all be the same?--> + <xml name="ref_sel"> + <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> + <option value="no_ref" selected="true">Do not pass</option> + </param> + <when value="cached"> + <param name="reference_sequence" type="select" label="Reference" help="Reference sequence file." > + <options from_data_table="all_fasta" > + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> + </options> + </param> + </when> + <when value="history"> + <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Reference sequence file." /> + </when> + <when value="no_ref" /> + </conditional> + </xml> + + <template name="ref_opts"> + #for $sect in $sections + #if $varExists($sect + "reference_source.reference_source_selector") + #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref" + #if $getVar($sect + "reference_source.reference_source_selector") != "history" + --reference $getVar($sect + "reference_source.reference_sequence.fields.path") + #else + --reference reference.fa + #end if + #end if + #end if + #end for + </template> + + <template name="picard_ref_opts"> + #for $sect in $sections + #if $varExists($sect + "reference_source.reference_source_selector") + #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref" + #if $getVar($sect + "reference_source.reference_source_selector") != "history" + --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence.fields.path") + #else + --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence") + #end if + #end if + #end if + #end for + </template> + + <template name="picard_ref_opts_plain"> + #for $sect in $sections + #if $varExists($sect + "reference_source.reference_source_selector") + #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref" + #if $getVar($sect + "reference_source.reference_source_selector") != "history" + --REFERENCE $getVar($sect + "reference_source.reference_sequence.fields.path") + #else + --REFERENCE $getVar($sect + "reference_source.reference_sequence") + #end if + #end if + #end if + #end for + </template> + + <template name="ref_opts_input"> + #for $sect in $sections + #if $varExists($sect + "reference_source.reference_source_selector") + #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref" + #if $getVar($sect + "reference_source.reference_source_selector") != "history" + --input $getVar($sect + "reference_source.reference_sequence.fields.path") + #else + --input $getVar($sect + "reference_source.reference_sequence") + #end if + #end if + #end if + #end for + </template> + + + <!--Interval Macros--> + <template name="gatk_ints_chth"> + #for $sect in $sections + #if $varExists($sect + "ival_type.ival_type_sel") + #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file" + #if $varExists($sect + "ival_type.intervals") + #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval") + --intervals intervals.interval_list + #end if + #if $getVar($sect + "ival_type.intervals").is_of_type("bed") + --intervals intervals.bed + #end if + #if $getVar($sect + "ival_type.intervals").is_of_type("vcf") + --intervals intervals.vcf + #end if + #end if + #else + #if $varExists($sect + "ival_type.intervals") + --intervals $getVar($sect + "ival_type.intervals") + #end if + #end if + #if $varExists($sect + "ival_type.interval_padding") + --interval-padding $getVar($sect + "ival_type.interval_padding") + #end if + #end if + #end for + </template> + + + <template name="pre_gatk_ints_chth"><![CDATA[ + #for $sect in $sections + #if $varExists($sect + "ival_type.ival_type_sel") + #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file" + #if $varExists($sect + "ival_type.intervals") + #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval") + ln -s $getVar($sect + "ival_type.intervals") intervals.interval_list && + #end if + #if $getVar($sect + "ival_type.intervals").is_of_type("bed") + ln -s $getVar($sect + "ival_type.intervals") intervals.bed && + #end if + #if $getVar($sect + "ival_type.intervals").is_of_type("vcf") + ln -s $getVar($sect + "ival_type.intervals") intervals.vcf && + #end if + #end if + #end if + #end if + #end for + ]]></template> + + <xml name="gatk_ints"> + <conditional name="ival_type"> + <param name="ival_type_sel" type="select" label="Choose Genomic Interval Source"> + <option value="ival_file" selected="true">Interval File</option> + <option value="ival_text" selected="false">Interval Text Input</option> + </param> + <when value="ival_file"> + <param name="intervals" argument="--intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Intervals File" help="One or more genomic intervals over which to operate"/> + <param name="interval_padding" argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/> + </when> + <when value="ival_text"> + <param name="intervals" argument="--intervals" type="text" optional="true" label="Intervals Text Input" help="One or more genomic intervals over which to operate. Enter in chrom:start-stop format."/> + <param name="interval_padding" argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/> + </when> + </conditional> + </xml> + + + <!--Exclude Intervals--> + <xml name="gatk_excl_ints"> + <conditional name="excl_ival_type"> + <param name="excl_ival_type_sel" type="select" label="Choose Genomic Interval Exclusion Source"> + <option value="excl_ival_file" selected="true">Exclude Interval File</option> + <option value="excl_ival_text" selected="false">Exclude Interval Text Input</option> + </param> + <when value="excl_ival_file"> + <param name="exclude_intervals" argument="--exclude-intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Exclude Intervals File" help="One or more genomic intervals to exclude from processing"/> + <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/> + </when> + <when value="excl_ival_text"> + <param name="exclude_intervals" argument="--exclude-intervals" type="text" optional="true" label="Exclude Intervals Text Input" help="One or more genomic intervals to exclude from processing. Enter in chrom:start-stop format."/> + <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/> + </when> + </conditional> + </xml> + + <template name="gatk_excl_ints_chth"> + #for $sect in $sections + #if $varExists($sect + "excl_ival_type.excl_ival_type_sel") + #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "ival_file" + #if $varExists($sect + "excl_ival_type.exclude_intervals") + #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval") + --exclude-intervals excl_intervals.interval_list + #end if + #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed") + --exclude-intervals excl_intervals.bed + #end if + #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf") + --exclude-intervals excl_intervals.vcf + #end if + #end if + #elif $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_text" + #if $varExists($sect + "excl_ival_type.exclude_intervals") + --exclude-intervals $getVar($sect + "excl_ival_type.exclude_intervals") + #end if + #else + #pass + #end if + #if $varExists($sect + "excl_ival_type.interval_exclusion_padding") + --interval-exclusion-padding $getVar($sect + "excl_ival_type.interval_exclusion_padding") + #end if + #end if + #end for + </template> + + <template name="pre_gatk_excl_ints_chth"><![CDATA[ + #for $sect in $sections + #if $varExists($sect + "excl_ival_type.excl_ival_type_sel") + #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_file" + #if $varExists($sect + "excl_ival_type.exclude_intervals") + #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval") + ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.interval_list && + #end if + #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed") + ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.bed && + #end if + #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf") + ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.vcf && + #end if + #end if + #end if + #end if + #end for + ]]></template> + + <!--Sequence dictionary selection options for Picard type tools--> + <template name="picard_seqdict_opts"> + #for $sect in $sections + #if $varExists($sect + "seqdict_source.seqdict_source_selector") + #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict" + #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history" + #set seq_dict_loc = ''.join($getVar($sect + seqdict_source.seqdict_sequence).fields.path.split('.')[:-1]) + '.dict' + --SEQUENCE_DICTIONARY $seq_dict_loc + #else + --SEQUENCE_DICTIONARY $getVar($sect + "seqdict_source.seqdict_sequence") + #end if + #end if + #end if + #end for + </template> + + <template name="gatk_seqdict"> + #for $sect in $sections + #if $varExists($sect + "seqdict_source.seqdict_source_selector") + #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict" + #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history" + #set $seq_dict_loc = ''.join($getVar($sect + "seqdict_source.seqdict_sequence").fields.path.split('.')[:-1]) + '.dict' + --sequence-dictionary $seq_dict_loc + #else + --sequence-dictionary $getVar($sect + "seqdict_source.seqdict_sequence") + #end if + #end if + #end if + #end for + </template> + + <xml name="seq_dict_sel"> + <conditional name="seqdict_source"> + <param name="seqdict_source_selector" type="select" label="Choose the source for the sequence dictionary"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + <option value="no_seq_dict" selected="true">Do not pass</option> + </param> + <when value="cached"> + <param name="seqdict_sequence" type="select" label="Sequence Dictionary" help="Sequence dictionary file." > + <options from_data_table="all_fasta" > + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> + </options> + </param> + </when> + <when value="history"> + <param name="seqdict_sequence" type="data" format="txt" label="Sequence Dictionary" help="Sequence dictionary file. Must be in dict format." /> + </when> + <when value="no_seq_dict" /> + </conditional> + </xml> + + <!--BAM input--> + <template name="picard_bam_input"> + --INPUT input.bam + </template> + + <template name="gatk_bam_input"> + --input input.bam + </template> + + <template name="bam_index_pre_chth"><![CDATA[ + #for $sect in $sections + #if $varExists($sect + "input") + #if $getVar($sect + "input").is_of_type("bam") + ln -s $getVar($sect + "input") input.bam && + samtools index input.bam && + #else + ln -s $getVar($sect + "input") input.sam && + samtools view -bS input.sam -o input.bam && + samtools index input.bam && + #end if + #end if + #end for + ]]></template> + + <xml name="gatk_bam_req_params"> + <param argument="--input" type="data" format="bam,sam" label="Input BAM/SAM/CRAM file" /> + </xml> + + <template name="picard_bam_index"><![CDATA[ + #if $input.is_of_type("bam") + ln -s $INPUT input.bam && + samtools index input.bam && + #else + ln -s $INPUT input.sam && + samtools view -bS input.sam -o input.bam && + samtools index input.bam && + #end if + ]]></template> + + + <!--Output goes to stdout, no output parameter exists.--> + <template name="stdout_to_output"> + > output.txt + </template> + + <xml name="stdout_to_output_params"> + <data format="txt" name="output" label="${tool.name} on ${on_string}: txt" from_work_dir="output.txt" /> + </xml> + + <!--Multiple input files, true for List[File] types, and sometimes List[String] types --> + <template name="gatk_input_multi"><![CDATA[ + #for $num, $file in enumerate($variant) + #if $file.is_of_type("vcf_bgzip") + --variant input${num}.vcf.gz + #elif $file.is_of_type("txt") + --variant input${num}.list + #else + --variant input${num}.vcf + #end if + #end for + ]]></template> + + <!--Multiple input files, true for List[File] types, and sometimes List[String] types --> + <template name="gatk_input_single"><![CDATA[ + #if $variant.is_of_type("vcf_bgzip") + --variant input${num}.vcf.gz + #elif $variant.is_of_type("txt") + --variant input${num}.list + #else + --variant input${num}.vcf + #end if + ]]></template> + + <template name="gatk_tabix_multi"><![CDATA[ + #for $num, $file in enumerate($variant) + #set datatype = $file.datatype + #if $file.is_of_type("vcf_bgzip") + ln -s $file input${num}.vcf.gz && + tabix input${num}.vcf.gz && + #elif $file.is_of_type("txt") + ln -s $file input${num}.list && + #else + ln -s $file input${num}.vcf && + #end if + #end for + ]]></template> + + <xml name="vcf_input_params_multi"> + <param name="input" type="data" multiple="true" format="vcf,vcf_bgzip" label="Input VCF file" help="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)"/> + </xml> + + + + <!--ABOVE HAS BEEN REVIEWED--> + + + + + + + + + + + <!--{--> + <!--"summary": "BAM/SAM/CRAM file containing reads",--> + <!--"name": "--input",--> + <!--"synonyms": "-I",--> + <!--"type": "List[String]",--> + <!--"required": "yes",--> + <!--"fulltext": "",--> + <!--"defaultValue": "[]",--> + <!--"minValue": "NA",--> + <!--"maxValue": "NA",--> + <!--"minRecValue": "NA",--> + <!--"maxRecValue": "NA",--> + <!--"kind": "required",--> + <!--"options": []--> + <!--},--> + <!--Required BAM input, GATK tool, may be specified multiple times.--> + <!--BAM should be indexed on the fly.--> + <!--Parameter is required, so is not contained within a section.--> + <!--Only decriptor that makes this unique for all input parameters is the summary field.--> + <!--{'pre_chth': ['bam_index_pre_chth'],--> + <!--'main_chth': ['picard_bam_input'],--> + <!--'main_xml': ['gatk_bam_req_params']}},--> + + + + + + + + + + + + + + <!--Macros for multiple input tools. List[File] in GATK json.--> + <template name="vcf_tabix_multi"><![CDATA[ + #for $num, $file in enumerate($input) + #set datatype = $file.datatype + #if $file.is_of_type("vcf_bgzip") + ln -s $file input${num}.vcf.gz && + tabix input${num}.vcf.gz && + #else + ln -s $file input${num}.vcf && + #end if + #end for + ]]></template> + + <template name="vcf_input_multi_picard"><![CDATA[ + #for $num, $file in enumerate($input) + #if $file.is_of_type("vcf_bgzip") + --INPUT input${num}.vcf.gz + #else + --INPUT input${num}.vcf + #end if + #end for + ]]></template> + + <template name="vcf_input_multi"><![CDATA[ + #for $num, $file in enumerate($input) + #if $file.is_of_type("vcf_bgzip") + --input input${num}.vcf.gz + #else + --input input${num}.vcf + #end if + #end for + ]]></template> + + + <!--Picard single input tools--> + <template name="vcf_tabix"><![CDATA[ + #set datatype = $input.datatype + #if $input.is_of_type("vcf_bgzip") + ln -s $input input.vcf.gz && + tabix input.vcf.gz && + #else + ln -s $input input.vcf && + #end if + ]]></template> + + <template name="gatk_tabix"><![CDATA[ + #set datatype = $variant.datatype + #if $variant.is_of_type("vcf_bgzip") + ln -s $variant input.vcf.gz && + tabix input.vcf.gz && + #else + ln -s $variant input.vcf && + gatk IndexFeatureFile -F input.vcf && + #end if + ]]></template> + + <template name="vcf_input_picard"><![CDATA[ + #if $input.is_of_type("vcf_bgzip") + --INPUT input.vcf.gz + #else + --INPUT input.vcf + #end if + ]]></template> + + <template name="vcf_input"><![CDATA[ + #if $input.is_of_type("vcf_bgzip") + --input input.vcf.gz + #else + --input input.vcf + #end if + ]]></template> + + <template name="gatk_input"><![CDATA[ + #if $variant.is_of_type("vcf_bgzip") + --variant input.vcf.gz + #else + --variant input.vcf + #end if + ]]></template> + + <template name="gatk_gvcf_tabix"><![CDATA[ + #if $variant + ln -s $variant input.g.vcf && + #end if + ]]></template> + + <template name="gatk_gvcf_input"><![CDATA[ + --variant input.g.vcf + ]]></template> + + <xml name="gatk_gvcf_input_params"> + <param name="variant" type="data" multiple="false" format="vcf" label="Input gVCF file" help=""/> + </xml> + + <xml name="vcf_input_params"> + <param name="input" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)"/> + </xml> + + <xml name="gatk_vcf_input_params"> + <param name="variant" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="A VCF file containing variants."/> + </xml> + + <xml name="gatk_vcf_input_params_multi"> + <param name="variant" type="data" multiple="true" format="vcf,vcf_bgzip,txt" label="Input VCF file(s)" help="A VCF file containing variants or a list of VCFs. Can be specified multiple times."/> + </xml> + + <xml name="gatk_req_params"> + <param name="input" type="data" format="bam,sam,cram" label="Input BAM/SAM/CRAM file" /> + </xml> + + <!--HDF5 Inputs--> + + <xml name="hdf5_input"> + <param name="input" type="data" format="h5,tabular" label="Input TSV or HDF5" help="Input TSV or HDF5 file containing integer read counts in genomic intervals for a single case sample (output of CollectReadCounts)." /> + </xml> + + <template name="hdf5_input_chth"><![CDATA[ + --input "${input}" + ]]></template> + + <template name="hdf5_output_chth"> + --output "${output}" + </template> + + <xml name="hdf5_output"> + <data format="h5" name="output" label="${tool.name} on ${on_string}: HDF5" help="Output file for read counts." /> + </xml> + + <!--Output specific to ModelSegments. Files created based on prefix, so force that to be what we want, then pull important files with from_work_dir.--> + <!--${SAMPLE}.cr.seg--> + <!--${SAMPLE}.modelFinal.seg--> + <template name="modelsegments_chth"><![CDATA[ + --output "." + --output-prefix "modelsegments" + ]]></template> + + <xml name="modelsegments_output"> + <data format="tabular" name="cr_seg" label="${tool.name} on ${on_string}: cr.seg" help="Copy-ratio segments." from_work_dir="modelsegments.cr.seg"/> + <data format="tabular" name="modelfinal_seg" label="${tool.name} on ${on_string}: modelFinal.seg" help="Modeled Segments" from_work_dir="modelsegments.modelFinal.seg"/> + </xml> + + <!--deltaMAD.txt--> + <!--denoisedLimit4.png--> + <!--denoisedMAD.txt--> + <!--denoised.png--> + <!--scaledDeltaMAD.txt--> + <!--modeled.png--> + <!--standardizedMAD.txt--> + + <template name="plotmodeledsegments_chth"><![CDATA[ + --output "." + --output-prefix "plotmodeledsegments" + ]]></template> + + <xml name="plotmodeledsegments_output"> + <data format="png" name="modeled_png" label="${tool.name} on ${on_string}: modeled.png" help="Copy-Ratio Plot" from_work_dir="plotmodeledsegments.modeled.png"/> + </xml> + + <!--Common Picard options--> + <template name="picard_opts"> + #if $picard_adv.arguments_file + --arguments_file ${picard_adv.arguments_file} + #end if + --COMPRESSION_LEVEL ${picard_adv.COMPRESSION_LEVEL} + #if $picard_adv.GA4GH_CLIENT_SECRETS + --GA4GH_CLIENT_SECRETS ${picard_adv.GA4GH_CLIENT_SECRETS} + #end if + --MAX_RECORDS_IN_RAM ${picard_adv.MAX_RECORDS_IN_RAM} + --VALIDATION_STRINGENCY ${picard_adv.VALIDATION_STRINGENCY} + --VERBOSITY ${picard_adv.VERBOSITY} + ${picard_adv.CREATE_MD5_FILE} + ${picard_adv.USE_JDK_DEFLATER} + ${picard_adv.USE_JDK_INFLATER} + </template> + + <xml name="picard_params"> + <section name="picard_adv" title="Advanced Picard Options (Only change these if you know what you're doing.)" expanded="False"> + <param argument="--arguments_file" type="data" optional="true" format="txt" label="Arguments File" help="read one or more arguments files and add them to the command line" /> + <param argument="--COMPRESSION_LEVEL" type="integer" optional="true" value="5" min="1" max="9" label="Compression Level" help="Compression level for all compressed files created (e.g. BAM and VCF)." /> + <param argument="--CREATE_MD5_FILE" truevalue="--CREATE_MD5_FILE" falsevalue="" type="boolean" optional="true" checked="false" label="Create MD5 File" help="Whether to create an MD5 digest for any BAM or FASTQ files created." /> + <param argument="--GA4GH_CLIENT_SECRETS" type="data" format="json" optional="true" label="Ga4Gh Client Secrets" help="Google Genomics API client_secrets.json file path." /> + <param argument="--MAX_RECORDS_IN_RAM" type="integer" optional="true" value="500000" label="Max Records In Ram" help="When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed." /> + <param argument="--TMP_DIR" type="text" optional="true" label="Tmp Dir" help="One or more directories with space available to be used by this program for temporary storage of working files. Keep in mind, you must be able to access this directory from either your user, or from the Galaxy user, depending on your configuration." /> + <param argument="--USE_JDK_DEFLATER" truevalue="--USE_JDK_DEFLATER" falsevalue="" type="boolean" optional="true" checked="false" label="Use Jdk Deflater" help="Use the JDK Deflater instead of the Intel Deflater for writing compressed output" /> + <param argument="--USE_JDK_INFLATER" truevalue="--USE_JDK_INFLATER" falsevalue="" type="boolean" optional="true" checked="false" label="Use Jdk Inflater" help="Use the JDK Inflater instead of the Intel Inflater for reading compressed input" /> + <param argument="--VALIDATION_STRINGENCY" type="select" optional="true" label="Validation Stringency" help="Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded." > + <option value="STRICT" selected="true">STRICT</option> + <option value="LENIENT" selected="false">LENIENT</option> + <option value="SILENT" selected="false">SILENT</option> + </param> + <param argument="--VERBOSITY" type="select" optional="true" label="Verbosity" help="Control verbosity of logging." > + <option value="ERROR" selected="false">ERROR</option> + <option value="WARNING" selected="false">WARNING</option> + <option value="INFO" selected="true">INFO</option> + <option value="DEBUG" selected="false">DEBUG</option> + </param> + </section> + </xml> + + <!--Provides option to create gzipped output for VCF files--> + <xml name="gzip_vcf_params"> + <param name="gzipped_output" type="boolean" checked="true" label="GZIP Output?" help="If you would like gzipped output, check this box. In general, it would be preferable to do this, unless your downstream tool does not support handling of gzipped files." /> + </xml> + + <!--Output related Picard options--> + <xml name="gzip_vcf_output_params"> + <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string}: vcf" from_work_dir="output.vcf" > + <filter>not gzipped_output</filter> + </data> + <data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: vcf_bgzip" from_work_dir="output.vcf.gz" > + <filter>gzipped_output</filter> + </data> + </xml> + + + <!--These are the same, other than the capitalization of output, so maybe a better way to do this.--> + <template name="picard_vcf_output_opts"> + #if $gzipped_output + --OUTPUT output.vcf.gz + #else + --OUTPUT output.vcf + #end if + </template> + + <template name="vcf_output_opts"> + #if $gzipped_output + --output output.vcf.gz + #else + --output output.vcf + #end if + </template> + + <xml name="picard_output_params"> + <data format="txt" name="output_md5" label="${tool.name} on ${on_string}: md5sum(txt)" from_work_dir="output.bam.md5" > + <filter>picard_adv['CREATE_MD5_FILE']</filter> + </data> + </xml> + + + <!--<template name="ref_opts">--> + <!--#set $sections = ['optional','advanced','common','deprecated','']--> + <!--#silent $sys.stderr.write("I WOULD LIKE TO SHOW THE SECTION VARIABLE: '${sections}'\n")--> + <!--#for $sect in $sections--> + <!--#if $varExists('$sect.reference_source.reference_source_selector')--> + <!--#if $sect.reference_source.reference_source_selector != "no_ref"--> + <!--#if $sect.reference_source.reference_source_selector != "history"--> + <!----reference ${sect.reference_source.reference_sequence.fields.path}--> + <!--#else--> + <!----reference ${sect.reference_source.reference_sequence}--> + <!--#end if--> + <!--#end if--> + <!--#end if--> + <!--#end for--> + <!--</template>--> + + + <!--<template name="ref_opts_opt">--> + <!--#if $optional.reference_source.reference_source_selector != "no_ref"--> + <!--#if $optional.reference_source.reference_source_selector != "history"--> + <!----reference ${optional.reference_source.reference_sequence.fields.path}--> + <!--#else--> + <!----reference ${optional.reference_source.reference_sequence}--> + <!--#end if--> + <!--#end if--> + <!--</template>--> + + + <!--Citations--> + <xml name="citations"> + <citation type="doi">10.1101/gr.107524.110</citation> + <citation type="doi">10.1038/ng.806</citation> + <citation type="doi">10.1002/0471250953.bi1110s43</citation> + <citation type="doi">10.1101/201178</citation> + <yield /> + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-in2.dict Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,2 @@ +@HD VN:1.6 +@SQ SN:K03455 LN:9719 M5:c66838498aab02f786a6ec2f2d62cdc1 UR:file:/home/inithello/github-repos/tools-iuc/tools/gatk4/test-data/../input-data/reference.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out1.vcf Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,91 @@ +##fileformat=VCFv4.2 +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> +##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> +##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input input.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="October 29, 2019 1:13:39 PM EDT"> +##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> +##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> +##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> +##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals"> +##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles"> +##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact"> +##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> +##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> +##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors"> +##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> +##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact"> +##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors"> +##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing"> +##INFO=<ID=UNIQ_ALT_READ_COUNT,Number=1,Type=Integer,Description="Number of ALT reads with unique start and mate end positions at a variant site"> +##MutectVersion=2.2 +##contig=<ID=K03455,length=9719> +##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives. +##source=Mutect2 +##tumor_sample=SRR8525881 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 +K03455 4098 . T C . . DP=1;ECNT=12;MBQ=0,34;MFRL=0,158;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=3.58 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,0:0,1:0,0,1,0 +K03455 4145 . T C . . DP=4;ECNT=12;MBQ=0,27;MFRL=0,242;MMQ=60,60;MPOS=39;POPAF=7.30;TLOD=17.40 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,4:0.800:4:0,1:0,3:0,0,3,1 +K03455 4190 . A G . . DP=14;ECNT=12;MBQ=38,38;MFRL=290,278;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=50.12 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:2,12:0.786:14:0,4:1,8:0|1:4190_A_G:4190:2,0,10,2 +K03455 4209 . GC AC,AA . . DP=18;ECNT=12;MBQ=37,35,35;MFRL=200,295,290;MMQ=60,60,60;MPOS=10,43;POPAF=7.30,7.30;TLOD=13.72,52.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:1,4,13:0.263,0.632:18:1,2,4:0,2,9:1,0,15,2 +K03455 4233 . T C . . DP=24;ECNT=12;MBQ=38,39;MFRL=252,263;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=16.13 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:19,5:0.261:24:7,2:11,3:1|0:4190_A_G:4190:16,3,5,0 +K03455 4250 . G A . . DP=36;ECNT=12;MBQ=37,37;MFRL=273,201;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=4.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:33,2:0.088:35:15,2:16,0:29,4,2,0 +K03455 4259 . T A . . DP=40;ECNT=12;MBQ=35,35;MFRL=254,276;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=134.66 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:7,32:0.784:39:3,15:4,13:0|1:4259_T_A:4259:7,0,27,5 +K03455 4262 . A T . . DP=40;ECNT=12;MBQ=37,37;MFRL=276,254;MMQ=60,60;MPOS=48;POPAF=7.30;TLOD=23.11 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:32,7:0.216:39:16,3:13,4:1|0:4259_T_A:4259:27,5,7,0 +K03455 4268 . G A . . DP=40;ECNT=12;MBQ=34,37;MFRL=252,273;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=47.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:27,13:0.368:40:11,7:13,5:22,5,13,0 +K03455 4271 . A G . . DP=43;ECNT=12;MBQ=37,33;MFRL=250,287;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=28.52 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,9:0.244:43:14,7:15,2:29,5,9,0 +K03455 4277 . C T . . DP=46;ECNT=12;MBQ=37,37;MFRL=244,276;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=148.83 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:10,36:0.767:46:3,18:4,16:0|1:4259_T_A:4259:9,1,31,5 +K03455 4279 . GT AC,AT . . DP=47;ECNT=12;MBQ=37,35,36;MFRL=263,252,202;MMQ=60,60,60;MPOS=34,33;POPAF=7.30,7.30;TLOD=60.64,24.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:17,21,9:0.421,0.201:47:8,8,5:7,9,4:16,1,25,5 +K03455 4310 . C T . . DP=39;ECNT=15;MBQ=20,18;MFRL=229,290;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=7.48 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,4:0.141:38:18,0:12,2:21,13,1,3 +K03455 4313 . G A . . DP=37;ECNT=15;MBQ=20,32;MFRL=229,273;MMQ=60,60;MPOS=69;POPAF=7.30;TLOD=12.35 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:32,5:0.143:37:12,3:12,1:17,15,4,1 +K03455 4320 . G A . . DP=38;ECNT=15;MBQ=20,20;MFRL=252,263;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=26.00 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,7:0.237:38:16,1:12,3:17,14,3,4 +K03455 4330 . A G . . DP=42;ECNT=15;MBQ=20,38;MFRL=252,276;MMQ=60,60;MPOS=60;POPAF=7.30;TLOD=13.81 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:37,4:0.125:41:16,3:17,0:19,18,3,1 +K03455 4334 . A G . . DP=43;ECNT=15;MBQ=32,36;MFRL=263,254;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=14.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:38,5:0.150:43:17,2:18,3:21,17,1,4 +K03455 4340 . A G . . DP=45;ECNT=15;MBQ=37,20;MFRL=263,252;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=109.80 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:17,28:0.586:45:8,13:9,11:0|1:4340_A_G:4340:9,8,13,15 +K03455 4343 . C A . . DP=43;ECNT=15;MBQ=33,20;MFRL=263,229;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=109.80 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:17,26:0.586:43:7,12:6,10:0|1:4340_A_G:4340:9,8,11,15 +K03455 4345 . GC AT . . DP=47;ECNT=15;MBQ=20,37;MFRL=204,254;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=44.93 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,13:0.302:47:12,4:14,6:16,18,6,7 +K03455 4346 . C T . . DP=46;ECNT=15;MBQ=20,26;MFRL=197,276;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=13.91 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,4:0.146:35:11,2:10,0:14,17,3,1 +K03455 4358 . T C . . DP=45;ECNT=15;MBQ=20,35;MFRL=206,254;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=17.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:37,7:0.171:44:13,4:19,3:16,21,2,5 +K03455 4361 . GCT ACT,G . . DP=47;ECNT=15;MBQ=36,20,35;MFRL=237,208,247;MMQ=60,60,60;MPOS=32,32;POPAF=7.30,7.30;TLOD=101.55,49.01 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:6,28,13:0.573,0.289:47:3,9,4:2,13,7:4,2,16,25 +K03455 4364 . A AAG . . DP=49;ECNT=15;MBQ=33,35;MFRL=208,247;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=48.10 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:34,13:0.295:47:15,4:17,7:15,19,5,8 +K03455 4370 . A G . . DP=51;ECNT=15;MBQ=20,37;MFRL=197,291;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=64.46 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:30,20:0.466:50:10,8:13,12:13,17,7,13 +K03455 4376 . C T . . DP=53;ECNT=15;MBQ=29,25;MFRL=231,244;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=80.90 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:28,24:0.446:52:8,10:16,12:9,19,11,13 +K03455 4397 . T C . . DP=57;ECNT=15;MBQ=34,37;MFRL=291,247;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=66.78 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:32,19:0.381:51:9,8:17,9:15,17,9,10 +K03455 4416 . C T . . DP=65;ECNT=21;MBQ=37,37;MFRL=270,310;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=33.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:54,11:0.193:65:21,4:31,4:22,32,6,5 +K03455 4418 . A G . . DP=64;ECNT=21;MBQ=37,37;MFRL=287,229;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=6.89 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:61,3:0.066:64:24,3:35,0:26,35,1,2 +K03455 4421 . T C . . DP=64;ECNT=21;MBQ=35,38;MFRL=259,291;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=140.93 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:28,36:0.574:64:15,13:10,21:11,17,16,20 +K03455 4424 . T C . . DP=62;ECNT=21;MBQ=37,38;MFRL=251,291;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=104.68 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:32,29:0.498:61:14,9:12,17:12,20,14,15 +K03455 4430 . T C . . DP=62;ECNT=21;MBQ=37,38;MFRL=284,265;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=3.90 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:60,2:0.051:62:24,2:31,0:25,35,1,1 +K03455 4439 . A G . . DP=54;ECNT=21;MBQ=38,35;MFRL=291,241;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=18.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:48,6:0.115:54:21,2:24,4:21,27,2,4 +K03455 4442 . AG GA . . DP=53;ECNT=21;MBQ=38,33;MFRL=290,209;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=18.54 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:45,7:0.159:52:18,2:23,5:19,26,3,4 +K03455 4443 . G A . . DP=53;ECNT=21;MBQ=37,38;MFRL=282,297;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=75.44 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:26,22:0.454:48:12,9:10,10:10,16,11,11 +K03455 4448 . C A . . DP=51;ECNT=21;MBQ=38,20;MFRL=290,126;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=9.07 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:47,3:0.062:50:18,0:25,2:20,27,1,2 +K03455 4449 . C T . . DP=49;ECNT=21;MBQ=37,38;MFRL=209,323;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=90.60 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:25,24:0.511:49:11,10:13,13:11,14,11,13 +K03455 4460 . T C . . DP=46;ECNT=21;MBQ=37,37;MFRL=284,329;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=18.65 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:40,6:0.159:46:15,2:22,3:20,20,2,4 +K03455 4465 . T TGGCC . . DP=45;ECNT=21;MBQ=37,35;MFRL=310,176;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=26.99 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:35,8:0.170:43:12,6:21,1:17,18,4,4 +K03455 4466 . A G,AGTG . . DP=44;ECNT=21;MBQ=38,38,37;MFRL=322,227,176;MMQ=60,60,60;MPOS=29,22;POPAF=7.30,7.30;TLOD=12.11,28.32 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:30,4,8:0.136,0.190:42:10,1,6:16,3,1:15,15,5,7 +K03455 4478 . T C . . DP=33;ECNT=21;MBQ=37,33;MFRL=323,206;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=40.91 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:23,10:0.303:33:7,6:15,4:12,11,4,6 +K03455 4505 . A G . . DP=19;ECNT=21;MBQ=39,38;MFRL=394,323;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=67.71 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:3,16:0.810:19:2,5:1,8:2,1,11,5 +K03455 4508 . A T . . DP=17;ECNT=21;MBQ=39,35;MFRL=341,335;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=53.29 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:4,13:0.737:17:2,5:2,8:2,2,10,3 +K03455 4511 . G A . . DP=17;ECNT=21;MBQ=37,36;MFRL=394,329;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=58.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:3,14:0.789:17:2,4:1,7:2,1,10,4 +K03455 4526 . T C . . DP=13;ECNT=21;MBQ=0,36;MFRL=0,323;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=57.35 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,13:0.933:13:0,7:0,6:0,0,11,2 +K03455 4528 . T TCA . . DP=13;ECNT=21;MBQ=38,37;MFRL=323,421;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=5.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:11,2:0.200:13:5,1:4,1:0|1:4528_T_TCA:4528:10,1,1,1 +K03455 4530 . CTT C . . DP=13;ECNT=21;MBQ=35,38;MFRL=323,421;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=4,2;RU=T;STR;TLOD=6.12 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:10,2:0.213:12:5,1:4,1:0|1:4528_T_TCA:4528:9,1,1,1 +K03455 4532 . T C . . DP=13;ECNT=21;MBQ=0,33;MFRL=0,323;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=39.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,11:0.926:11:0,7:0,2:0,0,11,0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out2.vcf Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,84 @@ +##fileformat=VCFv4.2 +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> +##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> +##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --interval-set-rule UNION --interval-exclusion-padding 0 --input input.bam --read-validation-stringency SILENT --reference reference.fa --add-output-sam-program-record true --add-output-vcf-command-line true --verbosity ERROR --QUIET true --read-filter AmbiguousBaseReadFilter --read-filter FirstOfPairReadFilter --read-filter GoodCigarReadFilter --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-padding 0 --interval-merging-rule ALL --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --ambig-filter-frac 0.05 --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="October 29, 2019 1:14:20 PM EDT"> +##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> +##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> +##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> +##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals"> +##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles"> +##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact"> +##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> +##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> +##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors"> +##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> +##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact"> +##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors"> +##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing"> +##INFO=<ID=UNIQ_ALT_READ_COUNT,Number=1,Type=Integer,Description="Number of ALT reads with unique start and mate end positions at a variant site"> +##MutectVersion=2.2 +##contig=<ID=K03455,length=9719> +##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives. +##source=Mutect2 +##tumor_sample=SRR8525881 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 +K03455 4861 . A G . . DP=1;ECNT=14;MBQ=0,37;MFRL=0,400;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,1:0,0:0,0,1,0 +K03455 4918 . G A . . DP=7;ECNT=14;MBQ=38,37;MFRL=303,370;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=8.65 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:3,3:0.499:6:2,0:1,2:2,1,0,3 +K03455 4923 . A G . . DP=8;ECNT=14;MBQ=0,33;MFRL=0,314;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=34.22 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,8:0.900:8:0,3:0,3:0,0,3,5 +K03455 4949 . G A . . DP=12;ECNT=14;MBQ=38,37;MFRL=285,264;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=27.49 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:5,7:0.573:12:2,2:1,4:0|1:4949_G_A:4949:2,3,2,5 +K03455 4952 . C T . . DP=13;ECNT=14;MBQ=36,37;MFRL=285,264;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=27.48 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:5,7:0.573:12:1,2:2,5:0|1:4949_G_A:4949:2,3,2,5 +K03455 4988 . T C . . DP=22;ECNT=14;MBQ=36,38;MFRL=285,278;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=14.99 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:17,5:0.250:22:5,2:8,2:6,11,3,2 +K03455 4991 . T C . . DP=22;ECNT=14;MBQ=37,28;MFRL=271,309;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=4.85 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:20,2:0.125:22:8,0:10,1:9,11,0,2 +K03455 4996 . AC GA . . DP=25;ECNT=14;MBQ=38,32;MFRL=285,203;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=5.72 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:21,3:0.152:24:6,1:10,1:8,13,1,2 +K03455 4997 . C T,A . . DP=25;ECNT=14;MBQ=38,37,38;MFRL=282,292,264;MMQ=60,60,60;MPOS=10,31;POPAF=7.30,7.30;TLOD=8.86,34.99 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:8,3,13:0.148,0.517:24:4,0,5:3,2,8:5,3,5,11 +K03455 5004 . G A . . DP=26;ECNT=14;MBQ=37,36;MFRL=262,288;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=4.21 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:24,2:0.107:26:7,1:13,1:8,16,1,1 +K03455 5015 . A G . . DP=34;ECNT=14;MBQ=38,38;MFRL=269,258;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=88.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:10,22:0.677:32:4,5:6,16:4,6,5,17 +K03455 5018 . A G . . DP=34;ECNT=14;MBQ=38,38;MFRL=262,261;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=11.32 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:30,4:0.139:34:9,0:15,4:10,20,0,4 +K03455 5027 . G A . . DP=37;ECNT=14;MBQ=37,38;MFRL=260,229;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=12.64 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:31,5:0.157:36:10,0:18,5:0|1:5027_G_A:5027:10,21,0,5 +K03455 5036 . G A . . DP=36;ECNT=14;MBQ=39,38;MFRL=256,229;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=12.71 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:30,5:0.162:35:9,0:18,4:0|1:5027_G_A:5027:10,20,0,5 +K03455 5076 . A G . . DP=37;ECNT=27;MBQ=38,37;MFRL=278,190;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=15.35 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:31,5:0.158:36:5,0:25,5:0|1:5076_A_G:5076:5,26,0,5 +K03455 5098 . A G . . DP=42;ECNT=27;MBQ=38,38;MFRL=190,292;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=126.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:7,32:0.804:39:0,4:7,22:0,7,4,28 +K03455 5099 . C T . . DP=42;ECNT=27;MBQ=38,37;MFRL=292,190;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=22.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:34,7:0.186:41:4,0:28,6:0|1:5076_A_G:5076:4,30,0,7 +K03455 5121 . C T . . DP=41;ECNT=27;MBQ=37,38;MFRL=257,205;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=24.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:33,8:0.209:41:3,1:28,6:3,30,1,7 +K03455 5130 . TG CA . . DP=38;ECNT=27;MBQ=38,38;MFRL=194,275;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=122.82 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:8,30:0.778:38:0,0:7,28:0,8,2,28 +K03455 5131 . G A . . DP=38;ECNT=27;MBQ=0,38;MFRL=0,205;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=23.77 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,8:0.932:8:0,1:0,6:0,0,1,7 +K03455 5133 . T C . . DP=36;ECNT=27;MBQ=38,36;MFRL=293,216;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=31.26 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:27,9:0.268:36:2,0:23,8:0|1:5133_T_C:5133:2,25,0,9 +K03455 5137 . GG AG,AA . . DP=35;ECNT=27;MBQ=39,39,39;MFRL=194,216,337;MMQ=60,60,60;MPOS=34,28;POPAF=7.30,7.30;TLOD=31.44,66.06 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:8,9,18:0.270,0.495:35:0,0,1:7,8,16:0,8,1,26 +K03455 5146 . AGG A . . DP=33;ECNT=27;MBQ=38,38;MFRL=315,216;MMQ=60,60;MPOS=43;POPAF=7.30;RPA=4,2;RU=G;STR;TLOD=31.38 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:24,9:0.286:33:1,0:22,9:0|1:5133_T_C:5133:1,23,0,9 +K03455 5147 . G A . . DP=33;ECNT=27;MBQ=38,37;MFRL=181,343;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=66.04 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:7,17:0.694:24:0,0:6,13:0|1:5147_G_A:5147:0,7,1,16 +K03455 5153 . GGTTT G . . DP=29;ECNT=27;MBQ=38,38;MFRL=296,216;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=32.02 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:20,9:0.323:29:0,0:19,9:0|1:5133_T_C:5133:0,20,0,9 +K03455 5155 . T C . . DP=28;ECNT=27;MBQ=38,38;MFRL=169,331;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=49.64 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,13:0.669:19:0,0:6,12:0|1:5147_G_A:5147:0,6,0,13 +K03455 5156 . T A . . DP=28;ECNT=27;MBQ=38,37;MFRL=315,181;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=16.29 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:14,5:0.283:19:0,0:14,5:0|1:5156_T_A:5156:0,14,0,5 +K03455 5157 . T G . . DP=28;ECNT=27;MBQ=38,37;MFRL=181,331;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=49.65 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,13:0.703:18:0,0:5,13:0,5,0,13 +K03455 5169 . C T . . DP=20;ECNT=27;MBQ=39,39;MFRL=296,170;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=20.02 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:14,6:0.318:20:0,0:14,6:0,14,0,6 +K03455 5175 . A T . . DP=19;ECNT=27;MBQ=37,39;MFRL=203,299;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=34.23 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:10,9:0.476:19:0,0:9,9:0|1:5147_G_A:5147:0,10,0,9 +K03455 5177 . G C . . DP=18;ECNT=27;MBQ=39,37;MFRL=299,216;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=25.72 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:11,7:0.400:18:0,0:10,7:0|1:5133_T_C:5133:0,11,0,7 +K03455 5179 . CC AC,AA . . DP=17;ECNT=27;MBQ=39,36,39;MFRL=366,216,315;MMQ=60,60,60;MPOS=60,51;POPAF=7.30,7.30;TLOD=26.12,30.50 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:2,7,8:0.400,0.450:17:0,0,0:2,7,8:0,2,0,15 +K03455 5189 . G A . . DP=18;ECNT=27;MBQ=39,39;MFRL=203,315;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=30.08 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:10,8:0.450:18:1,0:9,8:1,9,0,8 +K03455 5190 . A G . . DP=18;ECNT=27;MBQ=39,20;MFRL=293,181;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=9.31 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:15,3:0.200:18:0,0:15,2:0|1:5156_T_A:5156:0,15,1,2 +K03455 5196 . T C . . DP=18;ECNT=27;MBQ=39,37;MFRL=293,181;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=9.19 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:15,3:0.200:18:0,1:15,2:0,15,1,2 +K03455 5220 . G A . . DP=16;ECNT=27;MBQ=38,38;MFRL=312,219;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=21.54 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:10,6:0.389:16:1,0:9,6:0|1:5220_G_A:5220:1,9,0,6 +K03455 5223 . T A . . DP=16;ECNT=27;MBQ=37,39;MFRL=293,181;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=9.40 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:13,3:0.222:16:0,1:13,2:0|1:5223_T_A:5223:0,13,1,2 +K03455 5230 . T C . . DP=16;ECNT=27;MBQ=38,39;MFRL=293,181;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=9.40 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:13,3:0.222:16:0,1:12,2:0|1:5223_T_A:5223:0,13,1,2 +K03455 5233 . G A . . DP=12;ECNT=27;MBQ=38,38;MFRL=293,216;MMQ=60,60;MPOS=11;POPAF=7.30;TLOD=18.49 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:7,5:0.429:12:0,0:6,5:0|1:5220_G_A:5220:1,6,0,5 +K03455 5236 . A G . . DP=12;ECNT=27;MBQ=37,38;MFRL=216,256;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=22.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,6:0.539:11:0,1:5,5:0,5,1,5 +K03455 5240 . C T . . DP=11;ECNT=27;MBQ=37,37;MFRL=219,162;MMQ=60,60;MPOS=-1;POPAF=7.30;TLOD=9.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:8,3:0.308:11:0,0:7,3:1,7,0,3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out3.vcf Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,66 @@ +##fileformat=VCFv4.2 +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> +##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> +##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --max-population-af 0.01 --downsampling-stride 1 --normal-lod 2.2 --base-quality-score-threshold 18 --native-pair-hmm-threads 1 --min-base-quality-score 10 --output output.vcf --max-reads-per-alignment-start 50 --interval-padding 0 --interval-merging-rule ALL --input input.bam --reference reference.fa --QUIET true --gcs-max-retries 20 --annotation StrandBiasBySample --annotation BaseQualityHistogram --annotation OrientationBiasReadCounts --annotation-group StandardMutectAnnotation --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --pcr-snv-qual 40 --pcr-indel-qual 40 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-exclusion-padding 0 --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="October 29, 2019 1:15:01 PM EDT"> +##INFO=<ID=BQHIST,Number=A,Type=Integer,Description="Base quality counts for each allele represented sparsely as alternating entries of qualities and counts for each allele.For example [10,1,0,20,0,1] means one ref base with quality 10 and one alt base with quality 20."> +##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> +##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> +##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> +##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals"> +##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles"> +##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact"> +##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> +##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> +##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors"> +##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> +##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact"> +##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors"> +##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing"> +##INFO=<ID=UNIQ_ALT_READ_COUNT,Number=1,Type=Integer,Description="Number of ALT reads with unique start and mate end positions at a variant site"> +##MutectVersion=2.2 +##contig=<ID=K03455,length=9719> +##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives. +##source=Mutect2 +##tumor_sample=SRR8525881 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 +K03455 2652 . G A . . BQHIST=16,1,0,18,9,0,20,25,0,29,5,0,32,20,0,33,12,0,34,2,0,37,27,0,38,13,0,39,13,0;DP=129;ECNT=6;MBQ=0,33;MFRL=0,273;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=571.21 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,129:0.992:129:0,57:0,60:0|1:2652_G_A:2652:0,0,115,14 +K03455 2660 . T C . . BQHIST=15,1,0,16,1,0,17,2,0,20,24,0,29,1,0,32,4,0,33,3,0,34,2,0,35,6,0,37,48,0,38,27,0,39,20,0;DP=162;ECNT=6;MBQ=0,37;MFRL=0,274;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=717.35 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,162:0.993:162:0,66:0,69:0|1:2652_G_A:2652:0,0,145,17 +K03455 2664 . A G . . BQHIST=18,0,2,19,0,2,20,0,27,30,0,3,32,0,15,33,0,13,34,0,1,35,0,4,36,0,1,37,0,17,38,0,65,39,0,13;DP=165;ECNT=6;MBQ=0,37;MFRL=0,273;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=572.42 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,165:0.993:165:0,80:0,79:0,0,148,17 +K03455 2669 . G A . . BQHIST=16,1,0,18,1,0,19,2,0,20,32,0,29,1,0,32,5,0,33,8,0,34,3,0,36,1,0,37,45,0,38,44,0,39,31,0;DP=177;ECNT=6;MBQ=0,37;MFRL=0,274;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=755.51 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,174:0.994:174:0,84:0,86:0|1:2652_G_A:2652:0,0,155,19 +K03455 2677 . A G . . BQHIST=15,3,0,17,1,0,18,1,0,19,4,0,20,35,2,33,6,0,34,9,0,36,2,0,37,29,0,38,36,0,39,55,2;DP=186;ECNT=6;MBQ=38,30;MFRL=273,240;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=5.37 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:181,4:0.024:185:83,2:89,2:162,19,3,1 +K03455 2720 . T C . . BQHIST=14,3,0,16,10,0,17,1,0,18,20,0,20,65,0,30,1,0,32,2,0,33,25,0,34,9,0,36,12,0,37,81,0,38,24,0,39,40,0;DP=339;ECNT=6;MBQ=0,36;MFRL=0,263;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=1040.98 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,295:0.996:295:0,120:0,139:0,0,250,45 +K03455 2797 . G A . . BQHIST=15,2,0,16,3,0,17,1,0,18,22,0,20,188,0,32,5,0,33,21,0,35,8,0,36,8,0,37,56,0,38,62,0,39,110,0;DP=521;ECNT=12;MBQ=0,35;MFRL=0,246;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=1710.50 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,497:0.998:497:0,245:0,213:0,0,334,163 +K03455 2831 . A T . . BQHIST=14,5,0,15,12,0,16,2,1,17,48,3,18,12,10,19,3,0,20,138,0,29,2,0,30,5,1,31,6,0,32,9,0,33,40,2,34,14,0,35,1,0,36,6,0,37,52,0,38,43,0,39,102,0;DP=534;ECNT=12;MBQ=33,18;MFRL=240,262;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=4.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:502,17:0.023:519:221,1:197,2:298,204,0,17 +K03455 2848 . T TA . . BQHIST=14,0,2,15,0,18,16,0,11,17,0,1,20,6,241,27,0,1,29,0,1,30,1,14,31,0,1,32,0,13,33,2,22,34,0,11,35,0,1,36,0,20,37,0,47,38,1,71,39,3,81;DP=596;ECNT=12;MBQ=30,30;MFRL=257,246;MMQ=60,60;MPOS=32;POPAF=7.30;RPA=6,7;RU=A;STR;TLOD=1256.09 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,560:0.982:573:6,264:7,260:8,5,299,261 +K03455 2849 . A AG . . BQHIST=14,0,8,15,0,1,16,0,2,17,0,1,18,0,16,19,1,0,20,2,269,27,0,1,29,0,2,30,1,8,31,0,2,32,0,4,33,0,17,34,1,6,35,0,4,36,0,33,37,1,38,38,0,100,39,2,62;DP=594;ECNT=12;MBQ=20,32;MFRL=245,276;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=3.21 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:577,8:0.012:585:285,2:261,5:309,268,4,4 +K03455 2872 . T A . . BQHIST=14,1,2,15,2,0,16,0,10,17,6,6,18,15,51,19,0,38,20,0,164,27,1,1,29,0,16,30,0,3,31,0,9,32,0,20,33,0,29,34,0,12,35,0,12,36,0,9,37,0,78,38,0,46,39,0,53;DP=620;ECNT=12;MBQ=29,18;MFRL=240,283;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.49 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:559,25:0.023:584:222,1:230,0:259,300,25,0 +K03455 2874 . C T . . BQHIST=16,0,6,17,1,5,18,0,53,19,0,13,20,0,199,29,0,4,30,0,2,31,0,11,32,0,31,33,0,40,34,0,13,35,0,12,36,0,11,37,0,85,38,0,53,39,0,50;DP=598;ECNT=12;MBQ=17,32;MFRL=360,241;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=2009.02 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,595:0.997:596:0,262:0,249:1,0,292,303 +K03455 2882 . G T . . BQHIST=14,1,0,16,5,0,17,7,0,18,21,0,19,12,0,20,194,0,29,2,0,30,4,0,31,4,1,32,3,0,33,25,0,34,1,0,35,19,0,36,11,0,37,82,0,38,50,0,39,111,0;DP=569;ECNT=12;MBQ=31,33;MFRL=360,246;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=1892.82 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,568:0.997:569:1,254:0,252:1,0,287,281 +K03455 2889 . G A . . BQHIST=14,0,11,15,0,1,16,0,4,17,0,4,18,0,13,19,0,17,20,0,189,29,0,1,30,0,3,31,0,1,32,0,7,33,2,31,34,1,4,35,0,9,36,0,14,37,1,76,38,1,70,39,2,94,40,0,1;DP=568;ECNT=12;MBQ=33,37;MFRL=249,308;MMQ=60,60;MPOS=53;POPAF=7.30;TLOD=8.92 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:552,7:0.016:559:244,4:256,3:282,270,6,1 +K03455 2891 . A G . . BQHIST=14,0,1,16,4,0,17,9,0,18,18,0,19,8,0,20,176,6,30,1,0,31,4,0,32,7,0,33,25,1,34,2,0,35,26,0,36,7,1,37,75,0,38,84,0,39,87,0;DP=564;ECNT=12;MBQ=35,20;MFRL=249,231;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=8.84 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:543,9:0.013:552:237,4:257,4:276,267,5,4 +K03455 2894 . T C . . BQHIST=14,1,0,15,5,0,16,4,0,17,13,0,18,32,0,19,4,0,20,160,0,27,1,0,29,3,0,30,5,0,32,5,0,33,24,0,34,12,0,35,5,0,36,8,0,37,81,0,38,68,0,39,113,0;DP=551;ECNT=12;MBQ=0,35;MFRL=0,250;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1769.47 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,551:0.998:551:0,236:0,249:0,0,280,271 +K03455 2906 . C T . . BQHIST=16,0,2,18,0,4,19,0,10,20,0,144,30,0,2,31,0,1,32,0,3,33,0,19,34,0,3,35,0,19,36,0,11,37,0,57,38,0,75,39,0,145;DP=495;ECNT=12;MBQ=0,37;MFRL=0,250;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2348.23 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,495:0.998:495:0,225:0,254:0|1:2906_C_T:2906:0,0,235,260 +K03455 2913 . G A . . BQHIST=18,4,0,19,5,0,20,132,0,29,1,0,30,2,0,31,2,0,32,2,0,33,17,0,34,1,0,35,4,0,36,1,0,37,62,0,38,65,0,39,182,0,40,4,0;DP=492;ECNT=12;MBQ=0,38;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2341.59 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,492:0.998:492:0,224:0,251:0|1:2906_C_T:2906:0,0,234,258 +K03455 2987 . C T . . BQHIST=16,0,3,17,0,3,19,0,11,20,0,15,30,0,2,31,0,9,32,0,7,33,0,31,34,0,8,35,0,9,36,0,1,37,0,47,38,0,34,39,0,39;DP=223;ECNT=4;MBQ=0,37;MFRL=0,264;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=847.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,219:0.995:219:0,99:0,103:0,0,86,133 +K03455 2992 . T G . . BQHIST=16,1,0,17,3,0,18,1,7,19,23,0,20,13,1,29,1,0,31,8,0,32,8,0,33,18,1,34,9,0,35,4,0,36,4,0,37,35,0,38,30,0,39,21,0;DP=206;ECNT=4;MBQ=36,18;MFRL=271,260;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.86 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:179,9:0.043:188:74,2:77,0:74,105,9,0 +K03455 3016 . C A . . BQHIST=14,0,2,15,0,2,18,6,26,29,0,1,30,0,3,32,0,5,33,1,12,34,0,2,35,0,2,36,0,8,37,0,5,38,0,16,39,0,4;DP=100;ECNT=4;MBQ=33,18;MFRL=276,255;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=5.62 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:88,7:0.081:95:24,1:34,0:61,27,7,0 +K03455 3020 . A G . . BQHIST=14,0,12,16,0,1,18,0,1,27,0,3,29,0,3,30,0,8,32,0,8,33,0,2,34,0,1,35,0,1,36,0,21,37,0,4,38,0,23,39,0,1;DP=95;ECNT=4;MBQ=0,36;MFRL=0,284;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=324.41 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,90:0.989:90:0,32:0,43:0,0,65,25
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out4.vcf Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,75 @@ +##fileformat=VCFv4.2 +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> +##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> +##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --max-population-af 0.01 --downsampling-stride 1 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --dont-trim-active-regions true --num-pruning-samples 1 --min-dangling-branch-length 4 --max-num-haplotypes-in-population 128 --min-pruning 2 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 1 --bam-writer-type CALLED_HAPLOTYPES --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --max-mnp-distance 1 --output output.vcf --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-padding 0 --interval-merging-rule ALL --input input.bam --reference reference.fa --QUIET true --gcs-max-retries 20 --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --pcr-snv-qual 40 --pcr-indel-qual 40 --callable-depth 10 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --recover-all-dangling-branches false --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --native-pair-hmm-use-double-precision false --dont-use-soft-clipped-bases false --emit-ref-confidence NONE --force-call-filtered-alleles false --force-active false --interval-set-rule UNION --interval-exclusion-padding 0 --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="October 29, 2019 1:15:43 PM EDT"> +##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> +##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> +##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> +##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals"> +##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles"> +##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact"> +##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> +##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> +##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors"> +##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> +##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact"> +##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors"> +##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing"> +##INFO=<ID=UNIQ_ALT_READ_COUNT,Number=1,Type=Integer,Description="Number of ALT reads with unique start and mate end positions at a variant site"> +##MutectVersion=2.2 +##contig=<ID=K03455,length=9719> +##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives. +##source=Mutect2 +##tumor_sample=SRR8525881 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 +K03455 6822 . GT AC . . DP=2;ECNT=1;MBQ=0,29;MFRL=0,117;MMQ=60,60;MPOS=79;POPAF=7.30;TLOD=8.52 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,2:0.750:2:0,0:0,2:0,0,0,2 +K03455 6902 . A C . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=65;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6905 . A G . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6911 . T C . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6917 . G A . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6920 . G A . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6923 . C T . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6931 . C A . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6936 . C G . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 7441 . A ACCT . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=-2147483648;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7443 . A AGTG . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=94;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7449 . G A . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=100;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7452 . GGA G . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=103;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7455 . A ATG . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=106;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7457 . TGA T . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=108;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7460 . CA C . . DP=1;ECNT=23;MBQ=0,37;MFRL=0,486;MMQ=60,60;MPOS=111;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7468 . CC TA . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=114;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7478 . C T . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=111;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7491 . A T . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=104;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7494 . A G . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=101;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7508 . GA AG . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=87;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7541 . C CGA . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=54;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7542 . AGT A . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=53;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7548 . C A . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=47;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7555 . GA AT . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=40;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7560 . TC GT . . DP=2;ECNT=23;MBQ=0,38;MFRL=0,586;MMQ=60,50;MPOS=35;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7568 . T C . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=-1073741804;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7571 . T C . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=24;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7581 . C A . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=14;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7584 . T C . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=11;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7603 . A AGGG . . DP=2;ECNT=23;MBQ=0,37;MFRL=0,586;MMQ=60,50;MPOS=-8;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7604 . T G . . DP=2;ECNT=23;MBQ=0,33;MFRL=0,586;MMQ=60,50;MPOS=-22;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7541_C_CGA:7541:0,0,0,2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out5-1.tabular Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,9721 @@ +#track graphType=line +Chromosome Start End Feature ActivityProfile +K03455 0 1 state 0.00000 +K03455 1 2 state 0.00000 +K03455 2 3 state 0.00000 +K03455 3 4 state 0.00000 +K03455 4 5 state 0.00000 +K03455 5 6 state 0.00000 +K03455 6 7 state 0.00000 +K03455 7 8 state 0.00000 +K03455 8 9 state 0.00000 +K03455 9 10 state 0.00000 +K03455 10 11 state 0.00000 +K03455 11 12 state 0.00000 +K03455 12 13 state 0.00000 +K03455 13 14 state 0.00000 +K03455 14 15 state 0.00000 +K03455 15 16 state 0.00000 +K03455 16 17 state 0.00000 +K03455 17 18 state 0.00000 +K03455 18 19 state 0.00000 +K03455 19 20 state 0.00000 +K03455 20 21 state 0.00000 +K03455 21 22 state 0.00000 +K03455 22 23 state 0.00000 +K03455 23 24 state 0.00000 +K03455 24 25 state 0.00000 +K03455 25 26 state 0.00000 +K03455 26 27 state 0.00000 +K03455 27 28 state 0.00000 +K03455 28 29 state 0.00000 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out5-2.tabular Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,70 @@ +#track graphType=line +Chromosome Start End Feature AssemblyRegions +K03455 0 1 end-marker 0.00000 +K03455 0 300 size=300 -1.00000 +K03455 300 301 end-marker 0.00000 +K03455 300 600 size=300 -1.00000 +K03455 600 601 end-marker 0.00000 +K03455 600 900 size=300 -1.00000 +K03455 900 901 end-marker 0.00000 +K03455 900 1200 size=300 -1.00000 +K03455 1200 1201 end-marker 0.00000 +K03455 1200 1500 size=300 -1.00000 +K03455 1500 1501 end-marker 0.00000 +K03455 1500 1800 size=300 -1.00000 +K03455 1800 1801 end-marker 0.00000 +K03455 1800 2057 size=257 -1.00000 +K03455 2057 2058 end-marker 0.00000 +K03455 2057 2342 size=285 1.00000 +K03455 2342 2343 end-marker 0.00000 +K03455 2342 2481 size=139 1.00000 +K03455 2481 2482 end-marker 0.00000 +K03455 2481 2781 size=300 -1.00000 +K03455 2781 2782 end-marker 0.00000 +K03455 2781 3081 size=300 -1.00000 +K03455 3081 3082 end-marker 0.00000 +K03455 3081 3381 size=300 -1.00000 +K03455 3381 3382 end-marker 0.00000 +K03455 3381 3681 size=300 -1.00000 +K03455 3681 3682 end-marker 0.00000 +K03455 3681 3981 size=300 -1.00000 +K03455 3981 3982 end-marker 0.00000 +K03455 3981 4281 size=300 -1.00000 +K03455 4281 4282 end-marker 0.00000 +K03455 4281 4581 size=300 -1.00000 +K03455 4581 4582 end-marker 0.00000 +K03455 4581 4881 size=300 -1.00000 +K03455 4881 4882 end-marker 0.00000 +K03455 4881 5181 size=300 -1.00000 +K03455 5181 5182 end-marker 0.00000 +K03455 5181 5481 size=300 -1.00000 +K03455 5481 5482 end-marker 0.00000 +K03455 5481 5781 size=300 -1.00000 +K03455 5781 5782 end-marker 0.00000 +K03455 5781 6081 size=300 -1.00000 +K03455 6081 6082 end-marker 0.00000 +K03455 6081 6381 size=300 -1.00000 +K03455 6381 6382 end-marker 0.00000 +K03455 6381 6681 size=300 -1.00000 +K03455 6681 6682 end-marker 0.00000 +K03455 6681 6981 size=300 -1.00000 +K03455 6981 6982 end-marker 0.00000 +K03455 6981 7281 size=300 -1.00000 +K03455 7281 7282 end-marker 0.00000 +K03455 7281 7581 size=300 -1.00000 +K03455 7581 7582 end-marker 0.00000 +K03455 7581 7881 size=300 -1.00000 +K03455 7881 7882 end-marker 0.00000 +K03455 7881 8181 size=300 -1.00000 +K03455 8181 8182 end-marker 0.00000 +K03455 8181 8481 size=300 -1.00000 +K03455 8481 8482 end-marker 0.00000 +K03455 8481 8781 size=300 -1.00000 +K03455 8781 8782 end-marker 0.00000 +K03455 8781 9081 size=300 -1.00000 +K03455 9081 9082 end-marker 0.00000 +K03455 9081 9381 size=300 -1.00000 +K03455 9381 9382 end-marker 0.00000 +K03455 9381 9681 size=300 -1.00000 +K03455 9681 9682 end-marker 0.00000 +K03455 9681 9719 size=38 -1.00000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out5.vcf Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,93 @@ +##fileformat=VCFv4.2 +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> +##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> +##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --bam-output debug.bam --output output.vcf --activity-profile-out activity-profile.tab --assembly-region-out assembly-region.tab --input input.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="October 29, 2019 2:55:53 PM EDT"> +##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> +##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> +##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> +##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals"> +##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles"> +##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact"> +##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> +##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> +##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors"> +##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> +##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact"> +##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors"> +##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing"> +##INFO=<ID=UNIQ_ALT_READ_COUNT,Number=1,Type=Integer,Description="Number of ALT reads with unique start and mate end positions at a variant site"> +##MutectVersion=2.2 +##contig=<ID=K03455,length=9719> +##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives. +##source=Mutect2 +##tumor_sample=SRR8525881 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 +K03455 2097 . G A . . DP=14;ECNT=41;MBQ=0,20;MFRL=0,160;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=75.39 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,14:0.929:14:0,7:0,5:0,0,9,5 +K03455 2106 . T C . . DP=16;ECNT=41;MBQ=20,30;MFRL=160,90;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=12.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:12,4:0.266:16:6,1:6,1:8,4,2,2 +K03455 2110 . TA CA,CT . . DP=17;ECNT=41;MBQ=0,20,35;MFRL=0,159,161;MMQ=60,60,60;MPOS=42,2;POPAF=7.30,7.30;TLOD=55.54,10.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:0,13,4:0.754,0.187:17:0,6,1:0,7,3:0,0,11,6 +K03455 2118 . A G . . DP=17;ECNT=41;MBQ=32,20;MFRL=90,197;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=30.61 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,10:0.715:15:1,4:4,5:3,2,7,3 +K03455 2130 . T C . . DP=17;ECNT=41;MBQ=20,37;MFRL=159,161;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=10.45 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,4:0.199:17:4,1:8,3:8,5,3,1 +K03455 2136 . T C . . DP=17;ECNT=41;MBQ=20,38;MFRL=159,161;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=10.45 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:13,4:0.199:17:4,1:9,2:8,5,3,1 +K03455 2155 . A T . . DP=19;ECNT=41;MBQ=39,20;MFRL=90,234;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=39.43 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,14:0.777:19:1,5:4,6:3,2,10,4 +K03455 2169 . A G . . DP=22;ECNT=41;MBQ=0,35;MFRL=0,233;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=100.81 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,22:0.955:22:0,9:0,12:0,0,16,6 +K03455 2183 . C T . . DP=27;ECNT=41;MBQ=0,33;MFRL=0,233;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=129.24 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,27:0.962:27:0,9:0,13:0,0,18,9 +K03455 2189 . TA AA,AG . . DP=29;ECNT=41;MBQ=0,36,20;MFRL=0,232,265;MMQ=60,60,60;MPOS=25,22;POPAF=7.30,7.30;TLOD=46.72,54.99 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:0,13,14:0.424,0.539:27:0,6,5:0,6,5:0,0,18,9 +K03455 2195 . C G,T . . DP=29;ECNT=41;MBQ=37,30,35;MFRL=232,265,245;MMQ=60,60,60;MPOS=19,23;POPAF=7.30,7.30;TLOD=41.44,16.79 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:9,14,6:0.500,0.250:29:3,8,3:5,6,3:5,4,14,6 +K03455 2197 . A G . . DP=29;ECNT=41;MBQ=31,37;MFRL=257,232;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=29.34 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:20,9:0.259:29:9,3:7,5:14,6,5,4 +K03455 2200 . ACTC A . . DP=30;ECNT=41;MBQ=31,36;MFRL=265,232;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=13.22 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:23,5:0.153:28:10,3:6,2:0|1:2200_ACTC_A:2200:15,8,3,2 +K03455 2202 . T C . . DP=30;ECNT=41;MBQ=35,35;MFRL=265,182;MMQ=60,60;MPOS=12;POPAF=7.30;TLOD=5.58 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:21,4:0.166:25:9,1:7,1:0|1:2202_T_C:2202:14,7,2,2 +K03455 2205 . C A . . DP=30;ECNT=41;MBQ=36,26;MFRL=254,286;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=5.06 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:28,2:0.107:30:13,1:10,0:0|1:2202_T_C:2202:19,9,1,1 +K03455 2213 . A G . . DP=31;ECNT=41;MBQ=38,37;MFRL=232,265;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=102.83 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:7,24:0.793:31:4,11:2,8:4,3,17,7 +K03455 2214 . G A . . DP=28;ECNT=41;MBQ=33,26;MFRL=254,286;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=5.06 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:26,2:0.107:28:12,1:10,0:0|1:2214_G_A:2214:17,9,1,1 +K03455 2221 . C A . . DP=35;ECNT=41;MBQ=34,35;MFRL=251,232;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=12.67 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:30,5:0.114:35:16,1:11,2:0|1:2200_ACTC_A:2200:22,8,3,2 +K03455 2223 . G A . . DP=35;ECNT=41;MBQ=37,34;MFRL=251,211;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=47.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:20,14:0.446:34:12,7:7,6:17,3,7,7 +K03455 2224 . AT GG,CT . . DP=34;ECNT=41;MBQ=34,33,38;MFRL=265,212,253;MMQ=60,60,60;MPOS=37,18;POPAF=7.30,7.30;TLOD=13.11,33.64 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:19,5,10:0.118,0.324:34:9,3,7:8,2,3:11,8,13,2 +K03455 2225 . T G . . DP=34;ECNT=41;MBQ=37,38;MFRL=253,286;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=5.10 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:27,2:0.099:29:16,1:11,1:0|1:2214_G_A:2214:20,7,1,1 +K03455 2226 . A G . . DP=34;ECNT=41;MBQ=20,37;MFRL=232,253;MMQ=60,60;MPOS=20;POPAF=7.30;TLOD=114.56 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:7,27:0.818:34:4,16:2,9:0|1:2226_A_G:2226:4,3,20,7 +K03455 2230 . A C . . DP=36;ECNT=41;MBQ=28,37;MFRL=232,253;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=118.22 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:8,28:0.800:36:3,15:3,11:0|1:2226_A_G:2226:4,4,21,7 +K03455 2234 . A G . . DP=42;ECNT=41;MBQ=29,37;MFRL=232,245;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=144.85 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:8,34:0.821:42:2,20:3,11:0|1:2226_A_G:2226:4,4,24,10 +K03455 2235 . AC GA . . DP=42;ECNT=41;MBQ=36,34;MFRL=248,212;MMQ=60,60;MPOS=48;POPAF=7.30;TLOD=12.53 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:37,5:0.103:42:22,2:11,2:0|1:2200_ACTC_A:2200:25,12,3,2 +K03455 2236 . CTG C,GTG . . DP=42;ECNT=41;MBQ=38,35,38;MFRL=251,240,286;MMQ=60,60,60;MPOS=16,46;POPAF=7.30,7.30;TLOD=61.99,5.13 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:14,20,2:0.528,0.082:36:8,12,1:5,8,1:12,2,13,9 +K03455 2239 . TA CC . . DP=45;ECNT=41;MBQ=36,38;MFRL=232,251;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=48.80 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:29,14:0.350:43:15,9:10,4:17,12,12,2 +K03455 2240 . A ACC . . DP=45;ECNT=41;MBQ=37,34;MFRL=232,211;MMQ=60,60;MPOS=-2147483648;POPAF=7.30;TLOD=61.64 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:9,24:0.731:33:4,13:4,9:5,4,14,10 +K03455 2248 . A G . . DP=46;ECNT=41;MBQ=20,38;MFRL=197,247;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=185.50 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:6,40:0.884:46:3,21:3,16:1|0:2200_ACTC_A:2200:4,2,27,13 +K03455 2250 . T C . . DP=46;ECNT=41;MBQ=38,37;MFRL=247,197;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=15.87 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:40,6:0.116:46:23,3:16,3:0|1:2200_ACTC_A:2200:27,13,4,2 +K03455 2258 . GG AA . . DP=48;ECNT=41;MBQ=38,39;MFRL=241,235;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=163.72 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:7,41:0.843:48:3,23:3,17:0|1:2258_GG_AA:2258:6,1,27,14 +K03455 2259 . G A . . DP=48;ECNT=41;MBQ=0,37;MFRL=0,242;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=17.05 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 1|0:0,14:0.919:14:0,5:0,8:1|0:2258_GG_AA:2258:0,0,10,4 +K03455 2282 . C T . . DP=62;ECNT=41;MBQ=35,20;MFRL=241,182;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=12.25 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:57,5:0.075:62:24,2:24,2:32,25,3,2 +K03455 2285 . C T . . DP=65;ECNT=41;MBQ=28,38;MFRL=239,209;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=30.08 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:54,10:0.164:64:24,4:21,4:30,24,7,3 +K03455 2287 . CA AT . . DP=68;ECNT=41;MBQ=33,37;MFRL=232,285;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=17.29 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:61,7:0.128:68:26,1:25,2:33,28,4,3 +K03455 2300 . G A . . DP=67;ECNT=41;MBQ=31,32;MFRL=219,236;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=209.86 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:16,49:0.754:65:5,20:7,22:8,8,26,23 +K03455 2303 . GCA G . . DP=65;ECNT=41;MBQ=36,31;MFRL=221,241;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=170.03 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:19,45:0.695:64:4,18:11,20:9,10,25,20 +K03455 2304 . CAA GTG . . DP=65;ECNT=41;MBQ=33,20;MFRL=219,235;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=3.43 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:16,19:0.471:35:6,4:9,12:8,8,10,9 +K03455 2306 . A ATG,G . . DP=64;ECNT=41;MBQ=20,32,33;MFRL=188,239,274;MMQ=60,60,60;MPOS=39,19;POPAF=7.30,7.30;TLOD=174.74,25.23 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:7,48,9:0.738,0.173:64:4,20,2:3,23,5:4,3,30,27 +K03455 2315 . A G . . DP=63;ECNT=41;MBQ=37,38;MFRL=219,244;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=74.04 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:42,20:0.358:62:18,6:17,14:0|1:2315_A_G:2315:21,21,11,9 +K03455 2321 . A C . . DP=60;ECNT=41;MBQ=33,37;MFRL=212,244;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=74.63 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:39,20:0.377:59:18,6:18,14:0|1:2315_A_G:2315:19,20,11,9 +K03455 2349 . T C . . DP=53;ECNT=9;MBQ=34,35;MFRL=234,259;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=21.63 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:46,7:0.160:53:18,3:22,4:24,22,3,4 +K03455 2360 . G A . . DP=48;ECNT=9;MBQ=37,34;MFRL=235,232;MMQ=60,60;MPOS=43;POPAF=7.30;TLOD=20.61 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:41,7:0.175:48:16,3:22,3:22,19,3,4 +K03455 2362 . G A . . DP=48;ECNT=9;MBQ=0,37;MFRL=0,234;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=178.56 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,46:0.978:46:0,20:0,24:0,0,23,23 +K03455 2372 . A G . . DP=43;ECNT=9;MBQ=37,36;MFRL=237,227;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=22.64 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:36,7:0.192:43:8,2:17,4:19,17,3,4 +K03455 2374 . G A . . DP=34;ECNT=9;MBQ=37,37;MFRL=227,255;MMQ=60,60;MPOS=9;POPAF=7.30;TLOD=4.41 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:31,3:0.102:34:8,0:18,2:11,20,2,1 +K03455 2423 . A G . . DP=14;ECNT=9;MBQ=34,36;MFRL=248,221;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=5.14 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:12,2:0.187:14:3,0:8,2:0,12,0,2 +K03455 2436 . A G . . DP=4;ECNT=9;MBQ=16,33;MFRL=255,255;MMQ=60,60;MPOS=4;POPAF=7.30;TLOD=12.21 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:1,3:0.671:4:0,0:0,3:0,1,0,3 +K03455 2438 . A G . . DP=4;ECNT=9;MBQ=24,33;MFRL=255,255;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=7.53 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:2,2:0.502:4:0,0:1,2:0|1:2438_A_G:2438:0,2,0,2 +K03455 2440 . T C . . DP=4;ECNT=9;MBQ=0,31;MFRL=255,255;MMQ=60,60;MPOS=1;POPAF=7.30;TLOD=7.53 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:2,2:0.502:4:0,0:0,2:0|1:2438_A_G:2438:0,2,0,2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fa Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,2 @@ +>K03455 +TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables>