| Previous changeset 0:f41a1e03538b (2019-10-30) Next changeset 2:3be27a9a7313 (2020-04-10) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516" |
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modified:
gatk4_Mutect2.xml macros.xml test-data/Mutect2-out1.vcf test-data/Mutect2-out2.vcf test-data/Mutect2-out3.vcf test-data/Mutect2-out4.vcf test-data/Mutect2-out5.vcf |
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| diff -r f41a1e03538b -r fd2d6e035c3f gatk4_Mutect2.xml --- a/gatk4_Mutect2.xml Wed Oct 30 15:33:59 2019 -0400 +++ b/gatk4_Mutect2.xml Mon Nov 18 13:45:47 2019 -0500 |
| b |
| b'@@ -1,4 +1,4 @@\n-<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@0" profile="18.05">\n+<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@1" profile="18.05">\n <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>\n <macros>\n <import>macros.xml</import>\n@@ -62,16 +62,6 @@\n #end if\n #end if\n \n- #if $optional.population_callset\n- #set datatype = $optional.population_callset.datatype\n- #if $optional.population_callset.is_of_type("vcf_bgzip")\n- ln -s \'$optional.population_callset\' population_callset.vcf.gz &&\n- tabix population_callset.vcf.gz &&\n- #else\n- ln -s \'$optional.population_callset\' population_callset.vcf &&\n- #end if\n- #end if\n-\n #if $optional.alleles\n #set datatype = $optional.alleles.datatype\n #if $optional.alleles.is_of_type("vcf_bgzip")\n@@ -90,34 +80,6 @@\n \n #include source=$gatk_bam_input#\n \n- ## COMMON PARAMETERS ##\n-\n- #if str($common.common_parameters) == \'yes\'\n-\n- #if $common.read_filter\n- #for $filter in str($common.read_filter).split(\',\')\n- --read-filter="$filter"\n- #end for\n- #end if\n-\n- #if $common.disable_read_filter\n- #for $filter in str($common.disable_read_filter).split(\',\')\n- --disable-read-filter="$filter"\n- #end for\n- #end if\n-\n- --verbosity="ERROR"\n- --read-validation-stringency="$common.read_validation_stringency"\n- --interval-set-rule="$common.interval_set_rule"\n- $common.lenient\n- $common.disable_tool_default_read_filters\n- $common.add_output_sam_program_record\n- $common.add_output_vcf_command_line\n-\n- #end if\n-\n- ## END COMMON PARAMETERS ##\n-\n ## OPTIONAL PARAMETERS ##\n \n #if str($optional.optional_parameters) == \'yes\'\n@@ -172,26 +134,71 @@\n --alleles alleles.vcf\n #end if\n \n+ #if $optional.f1r2_max_depth:\n+ --f1r2-max-depth="$optional.f1r2_max_depth"\n+ #end if\n+\n+ #if $optional.f1r2_max_depth:\n+ --f1r2-median-mq="$optional.f1r2_median_mq"\n+ #end if\n+\n+ #if $optional.f1r2_max_depth:\n+ --f1r2-min-bq="$optional.f1r2_min_bq"\n+ #end if\n+\n+ #if $optional.interval_merging_rule:\n+ --interval-merging-rule="$optional.interval_merging_rule"\n+ #end if\n+\n+ #if $optional.interval_set_rule:\n+ --interval-set-rule="$optional.interval_set_rule"\n+ #end if\n+\n+ #if $optional.pcr_indel_qual:\n+ --pcr-indel-qual="$optional.pcr_indel_qual"\n+ #end if\n+\n+ #if $optional.pcr_snv_qual:\n+ --pcr-snv-qual="$optional.pcr_snv_qual"\n+ #end if\n+\n+ #if $optional.read_filter\n+ #for $filter in str($optional.read_filter).split(\',\')\n+ --read-filter="$filter"\n+ #end for\n+ #end if\n+\n+ #if $optional.disable_read_filter\n+ #for $filter in str($optional.disable_read_filter).split(\',\')\n+ --disable-read-filter="$filter"\n+ #end for\n+ #end if\n+\n --base-quality-score-threshold="$optional.base_quality_score_threshold"\n --af-of-alleles-not-in-resource="$optional.af_of_alleles_not_in_resource"\n --downsampling-stride="$optional.downsampling_stride"\n --gcs-max-retries="$optional.gcs_max_retries"\n --initial-tumor-lod="$optional.initial_tumor_lod"\n- --interval-merging-rule="$optional.interval_mergi'..b' <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">\n@@ -531,6 +549,8 @@\n <option value="AGGRESSIVE">Aggressive</option>\n </param>\n <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"/>\n+ <param name="pruning_lod_threshold" argument="--pruning-lod-threshold" type="float" optional="true" value="2.302585092994046" label="Pruning LOD threshold" help="Likelihood ratio threshold for adaptive pruning algorithm" />\n+ <param name="recover_all_dangling_branches" argument="--recover-all-dangling-branches" type="boolean" truevalue="--recover-all-dangling-branches" falsevalue="" label="Recover all dangling branches" />\n <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">\n <option selected="true" value="FASTEST_AVAILABLE">Fastest available</option>\n <option value="AVX_ENABLED">AVX-Enabled</option>\n@@ -571,7 +591,6 @@\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n <param name="reference_source_selector" value="history" />\n- <param name="common_parameters" value="no" />\n <param name="optional_parameters" value="no" />\n <param name="advanced_parameters" value="no" />\n <param name="output_parameters" value="no" />\n@@ -582,7 +601,6 @@\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n <param name="reference_source_selector" value="history" />\n- <param name="common_parameters" value="yes" />\n <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" />\n <param name="seqdict_source" value="history" />\n <param name="seqdict_sequence" value="Mutect2-in2.dict" />\n@@ -596,7 +614,6 @@\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n <param name="reference_source_selector" value="history" />\n- <param name="common_parameters" value="no" />\n <param name="optional_parameters" value="yes" />\n <param name="annotation" value="StrandBiasBySample,BaseQualityHistogram,OrientationBiasReadCounts" />\n <param name="annotation_group" value="StandardMutectAnnotation" />\n@@ -609,7 +626,6 @@\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n <param name="reference_source_selector" value="history" />\n- <param name="common_parameters" value="no" />\n <param name="optional_parameters" value="yes" />\n <param name="advanced_parameters" value="yes" />\n <param name="dont_trim_active_regions" value="true" />\n@@ -621,7 +637,6 @@\n <param name="reference_sequence" ftype="fasta" value="reference.fa" />\n <param name="gzipped_output" value="false" />\n <param name="reference_source_selector" value="history" />\n- <param name="common_parameters" value="no" />\n <param name="optional_parameters" value="no" />\n <param name="advanced_parameters" value="no" />\n <param name="output_parameters" value="yes" />\n' |
| b |
| diff -r f41a1e03538b -r fd2d6e035c3f macros.xml --- a/macros.xml Wed Oct 30 15:33:59 2019 -0400 +++ b/macros.xml Mon Nov 18 13:45:47 2019 -0500 |
| [ |
| @@ -22,7 +22,7 @@ <!--Define sections that parameters could exist within.--> <template name="set_sections"> - #set global $sections = ['', 'optional.', 'advanced.', 'common.', 'deprecated.'] + #set global $sections = ['', 'optional.', 'advanced.', 'deprecated.'] </template> <!--Reference genome handling--> @@ -671,7 +671,7 @@ <!--<template name="ref_opts">--> - <!--#set $sections = ['optional','advanced','common','deprecated','']--> + <!--#set $sections = ['optional','advanced','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')--> |
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| diff -r f41a1e03538b -r fd2d6e035c3f test-data/Mutect2-out1.vcf --- a/test-data/Mutect2-out1.vcf Wed Oct 30 15:33:59 2019 -0400 +++ b/test-data/Mutect2-out1.vcf Mon Nov 18 13:45:47 2019 -0500 |
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| @@ -11,7 +11,7 @@ ##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"> +##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="November 15, 2019 4:24:40 PM EST"> ##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"> |
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| diff -r f41a1e03538b -r fd2d6e035c3f test-data/Mutect2-out2.vcf --- a/test-data/Mutect2-out2.vcf Wed Oct 30 15:33:59 2019 -0400 +++ b/test-data/Mutect2-out2.vcf Mon Nov 18 13:45:47 2019 -0500 |
| b |
| b'@@ -11,7 +11,7 @@\n ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">\n ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher\'s Exact Test to detect strand bias.">\n-##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">\n+##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --input input.bam --reference reference.fa --QUIET true --f1r2-median-mq 50 --f1r2-mi'..b':F2R1:SB\t0/1/2:11,16,2:0.591,0.064:29:4,2,0:7,14,2:2,9,1,17\n+K03455\t5169\t.\tC\tT\t.\t.\tDP=29;ECNT=29;MBQ=38,32;MFRL=275,190;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=39.25\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:18,11:0.379:29:2,4:15,7:1,17,1,10\n+K03455\t5175\t.\tA\tT\t.\t.\tDP=26;ECNT=29;MBQ=36,38;MFRL=222,293;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=52.80\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:13,13:0.481:26:3,2:9,11:0|1:5147_G_A:5147:0,13,1,12\n+K03455\t5177\t.\tG\tC\t.\t.\tDP=25;ECNT=29;MBQ=37,37;MFRL=293,219;MMQ=60,60;MPOS=58;POPAF=7.30;TLOD=28.74\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:17,8:0.346:25:4,1:12,7:0|1:5133_T_C:5133:1,16,0,8\n+K03455\t5179\t.\tCC\tAC,AA\t.\t.\tDP=24;ECNT=29;MBQ=38,34,38;MFRL=339,219,296;MMQ=60,60,60;MPOS=58,51;POPAF=7.30,7.30;TLOD=29.12,49.40\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1/2:4,8,12:0.346,0.462:24:2,1,2:2,7,10:0,4,1,19\n+K03455\t5189\t.\tG\tA\t.\t.\tDP=25;ECNT=29;MBQ=39,39;MFRL=222,296;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=48.64\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:13,12:0.462:25:4,2:9,10:1,12,1,11\n+K03455\t5190\t.\tA\tG\t.\t.\tDP=25;ECNT=29;MBQ=39,20;MFRL=252,278;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=15.35\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:20,5:0.231:25:3,2:17,2:0|1:5156_T_A:5156:1,19,1,4\n+K03455\t5196\t.\tT\tC\t.\t.\tDP=25;ECNT=29;MBQ=38,20;MFRL=246,339;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=6.08\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:21,4:0.191:25:3,3:18,1:1,20,1,3\n+K03455\t5220\t.\tG\tA\t.\t.\tDP=23;ECNT=29;MBQ=37,37;MFRL=286,222;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=24.08\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:16,7:0.344:23:5,1:11,6:0|1:5220_G_A:5220:2,14,0,7\n+K03455\t5223\t.\tT\tA\t.\t.\tDP=22;ECNT=29;MBQ=37,37;MFRL=257,278;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=17.15\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:17,5:0.269:22:2,3:14,2:0|1:5223_T_A:5223:1,16,1,4\n+K03455\t5226\t.\tT\tC\t.\t.\tDP=22;ECNT=29;MBQ=34,35;MFRL=268,253;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=12.23\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:16,6:0.231:22:4,1:12,5:1,15,1,5\n+K03455\t5230\t.\tT\tC\t.\t.\tDP=21;ECNT=29;MBQ=33,38;MFRL=275,278;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=17.08\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:16,5:0.281:21:2,3:13,2:0|1:5223_T_A:5223:1,15,1,4\n+K03455\t5233\t.\tG\tA\t.\t.\tDP=16;ECNT=29;MBQ=38,38;MFRL=293,216;MMQ=60,60;MPOS=11;POPAF=7.30;TLOD=17.95\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:11,5:0.369:16:3,0:7,5:0|1:5220_G_A:5220:2,9,0,5\n+K03455\t5236\t.\tA\tG\t.\t.\tDP=16;ECNT=29;MBQ=37,38;MFRL=216,293;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=40.42\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:5,11:0.631:16:0,4:5,6:0,5,2,9\n+K03455\t5240\t.\tC\tT\t.\t.\tDP=15;ECNT=29;MBQ=37,37;MFRL=250,162;MMQ=60,60;MPOS=-1;POPAF=7.30;TLOD=9.14\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:12,3:0.250:15:3,0:8,3:2,10,0,3\n+K03455\t6902\t.\tA\tC\t.\t.\tDP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=65;POPAF=7.30;TLOD=4.20\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1\n+K03455\t6905\t.\tA\tG\t.\t.\tDP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=4.20\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1\n+K03455\t6911\t.\tT\tC\t.\t.\tDP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.20\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1\n+K03455\t6917\t.\tG\tA\t.\t.\tDP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1\n+K03455\t6920\t.\tG\tA\t.\t.\tDP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=4.20\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1\n+K03455\t6923\t.\tC\tT\t.\t.\tDP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=4.20\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1\n+K03455\t6931\t.\tC\tA\t.\t.\tDP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.20\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1\n+K03455\t6936\t.\tC\tG\t.\t.\tDP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=4.20\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1\n' |
| b |
| diff -r f41a1e03538b -r fd2d6e035c3f test-data/Mutect2-out3.vcf --- a/test-data/Mutect2-out3.vcf Wed Oct 30 15:33:59 2019 -0400 +++ b/test-data/Mutect2-out3.vcf Mon Nov 18 13:45:47 2019 -0500 |
| [ |
| @@ -11,7 +11,7 @@ ##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"> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --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 --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-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --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 --gcs-max-retries 20 --annotation StrandBiasBySample --annotation BaseQualityHistogram --annotation OrientationBiasReadCounts --annotation-group StandardMutectAnnotation --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --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 --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-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="November 15, 2019 4:25:49 PM EST"> ##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"> |
| b |
| diff -r f41a1e03538b -r fd2d6e035c3f test-data/Mutect2-out4.vcf --- a/test-data/Mutect2-out4.vcf Wed Oct 30 15:33:59 2019 -0400 +++ b/test-data/Mutect2-out4.vcf Mon Nov 18 13:45:47 2019 -0500 |
| b |
| @@ -11,7 +11,7 @@ ##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"> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --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 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --minimum-allele-fraction 0.0 --dont-trim-active-regions true --num-pruning-samples 1 --min-dangling-branch-length 4 --max-num-haplotypes-in-population 128 --min-pruning 2 --pruning-lod-threshold 2.30258509299 --max-unpruned-variants 100 --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 --emit-ref-confidence NONE --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-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --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 --gcs-max-retries 20 --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --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 --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 --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 --force-call-filtered-alleles false --force-active false --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-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="November 15, 2019 4:26:31 PM EST"> ##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"> |
| b |
| diff -r f41a1e03538b -r fd2d6e035c3f test-data/Mutect2-out5.vcf --- a/test-data/Mutect2-out5.vcf Wed Oct 30 15:33:59 2019 -0400 +++ b/test-data/Mutect2-out5.vcf Mon Nov 18 13:45:47 2019 -0500 |
| b |
| @@ -11,7 +11,7 @@ ##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"> +##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="November 15, 2019 4:26:58 PM EST"> ##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"> |