| Next changeset 1:fd2d6e035c3f (2019-11-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" |
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added:
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 |
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| diff -r 000000000000 -r f41a1e03538b gatk4_Mutect2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gatk4_Mutect2.xml Wed Oct 30 15:33:59 2019 -0400 |
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| b'@@ -0,0 +1,758 @@\n+<tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@0" profile="18.05">\n+ <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="version_cmd"/>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ #include source=$set_sections#\n+ #include source=$pre_gatk_excl_ints_chth#\n+ #include source=$bam_index_pre_chth#\n+ #include source=$pre_gatk_ints_chth#\n+\n+ #set ref_flag=\'--reference="reference.fa"\'\n+\n+ #if str($reference_source.reference_source_selector) == \'history\'\n+ ln -s \'$reference_source.reference_sequence\' reference.fa &&\n+ samtools faidx reference.fa &&\n+ gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&\n+ #else if str($reference_source.reference_source_selector) == \'history\'\n+ ln -s \'$reference_source.reference_sequence.fields.path\' reference.fa &&\n+ samtools faidx reference.fa &&\n+ gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&\n+ #else\n+ #set ref_flag=\'\'\n+ #end if\n+\n+ #if str($outputs.output_parameters) == \'yes\'\n+ #if str($outputs.debug_activity) == \'yes\'\n+ ln -s \'$activity_profile_out\' activity-profile.tab &&\n+ #end if\n+ #if str($outputs.debug_assembly) == \'yes\'\n+ ln -s \'$assembly_region_out\' assembly-region.tab &&\n+ #end if\n+ #if str($outputs.debug_bam) == \'yes\'\n+ ln -s \'$bam_output\' debug.bam &&\n+ #end if\n+ #end if\n+\n+ @CMD_BEGIN@ GetSampleName --input="input.bam" --output="samplename.txt" &&\n+ sample=`cat samplename.txt` &&\n+\n+ #if str($optional.optional_parameters) == \'yes\'\n+ #if $optional.panel_of_normals\n+ #set datatype = $optional.panel_of_normals.datatype\n+ #if $optional.panel_of_normals.is_of_type("vcf_bgzip")\n+ ln -s \'$optional.panel_of_normals\' panel_of_normals.vcf.gz &&\n+ tabix panel_of_normals.vcf.gz &&\n+ #else\n+ ln -s \'$optional.panel_of_normals\' panel_of_normals.vcf &&\n+ #end if\n+ #end if\n+\n+ #if $optional.germline_resource\n+ #set datatype = $optional.germline_resource.datatype\n+ #if $optional.germline_resource.is_of_type("vcf_bgzip")\n+ ln -s \'$optional.germline_resource\' germline_resource.vcf.gz &&\n+ tabix germline_resource.vcf.gz &&\n+ #else\n+ ln -s \'$optional.germline_resource\' germline_resource.vcf &&\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 $optional.alleles.is_of_type("vcf_bgzip")\n+ ln -s \'$optional.alleles\' alleles.vcf.gz &&\n+ tabix alleles.vcf.gz &&\n+ @CMD_BEGIN@ IndexFeatureFile --feature-file alleles.vcf.gz &&\n+ #else\n+ ln -s \'$optional.alleles\' alleles.vcf &&\n+ @CMD_BEGIN@ IndexFeatureFile --feature-file alleles.vcf &&\n+ #end if\n+ #end if\n+\n+ #end i'..b'allset for\n+subsequent filtering and review.\n+\n+::\n+\n+ gatk Mutect2 \\\n+ -R reference.fa \\\n+ -I tumor.bam \\\n+ -tumor tumor_sample_name \\\n+ -I normal.bam \\\n+ -normal normal_sample_name \\\n+ --germline-resource af-only-gnomad.vcf.gz \\\n+ --af-of-alleles-not-in-resource 0.00003125 \\\n+ --panel-of-normals pon.vcf.gz \\\n+ -O somatic.vcf.gz\n+\n+\n+The --af-of-alleles-not-in-resource argument value should match\n+expectations for alleles not found in the provided germline resource.\n+Note the tool does not require a germline resource nor a panel of\n+normals (PoN) to run. The tool prefilters sites for the matched normal\n+and the PoN. For the germline resource, the tool prefilters on the\n+allele. Below is an excerpt of a known variants resource with population\n+allele frequencies\n+\n+::\n+\n+ #CHROM POS ID REF ALT QUAL FILTER INFO\n+ 1 10067 . T TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 30.35 PASS AC=3;AF=7.384E-5\n+ 1 10108 . CAACCCT C 46514.32 PASS AC=6;AF=1.525E-4\n+ 1 10109 . AACCCTAACCCT AAACCCT,* 89837.27 PASS AC=48,5;AF=0.001223,1.273E-4\n+ 1 10114 . TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA *,CAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA,T 36728.97 PASS AC=55,9,1;AF=0.001373,2.246E-4,2.496E-5\n+ 1 10119 . CT C,* 251.23 PASS AC=5,1;AF=1.249E-4,2.498E-5\n+ 1 10120 . TA CA,* 14928.74 PASS AC=10,6;AF=2.5E-4,1.5E-4\n+ 1 10128 . ACCCTAACCCTAACCCTAAC A,* 285.71 PASS AC=3,1;AF=7.58E-5,2.527E-5\n+ 1 10131 . CT C,* 378.93 PASS AC=7,5;AF=1.765E-4,1.261E-4\n+ 1 10132 . TAACCC *,T 18025.11 PASS AC=12,2;AF=3.03E-4,5.049E-5\n+\n+\n+(ii) Tumor-only mode\n+^^^^^^^^^^^^^^^^^^^^\n+\n+This mode runs on a single sample, e.g. single tumor or single normal\n+sample. To create a PoN, call on each normal sample in this mode, then\n+use CreateSomaticPanelOfNormals to generate the PoN.\n+\n+::\n+\n+ gatk Mutect2 \\\n+ -R reference.fa \\\n+ -I sample.bam \\\n+ -tumor sample_name \\\n+ -O single_sample.vcf.gz\n+\n+\n+Further points of interest\n+~~~~~~~~~~~~~~~~~~~~~~~~~~\n+\n+Additional parameters that factor towards filtering, including\n+normal-artifact-lod (default threshold 0.0) and tumor-lod (default\n+threshold 5.3), are available in FilterMutectCalls. While the tool\n+calculates normal-lod assuming a diploid genotype, it calculates\n+normal-artifact-lod with the same approach it uses for tumor-lod, i.e.\n+with a variable ploidy assumption.\n+\n+- 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.\n+\n+- 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.\n+\n+\n+If a variant is absent from a given germline resource, then the value\n+for --af-of-alleles-not-in-resource applies. For example, gnomAD\'s\n+16,000 samples (~32,000 homologs per locus) becomes a probability of one\n+in 32,000 or less. Thus, an allele\'s absence from the germline resource\n+becomes evidence that it is not a germline variant.\n+\n+Caveats\n+~~~~~~~\n+\n+Although GATK4 Mutect2 accomodates varying coverage depths, further\n+optimization of parameters may improve calling for extreme high depths,\n+e.g. 1000X.\n+]]></help>\n+ <citations>\n+ <expand macro="citations"/>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r f41a1e03538b macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Oct 30 15:33:59 2019 -0400 |
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| b'@@ -0,0 +1,710 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <token name="@VERSION@">4.1.4.0</token>\n+ <token name="@WRAPPER_VERSION@">@VERSION@+galaxy</token>\n+\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">gatk4</requirement>\n+ <requirement type="package" version="0.2.5">tabix</requirement>\n+ <requirement type="package" version="1.9">samtools</requirement>\n+ <yield />\n+ </requirements>\n+ </xml>\n+\n+ <!--Hacky way to determine GATK version, for display in tool info-->\n+ <xml name="version_cmd">\n+ <version_command>gatk SortSam --version 2>&1 | grep Version | cut -d \':\' -f 2</version_command>\n+ </xml>\n+\n+ <!--Command token, java options should not be hard coded here.-->\n+ <token name="@CMD_BEGIN@">[[ -z \\$_JAVA_OPTIONS ]] && export JAVA_OPTS=\\$_JAVA_OPTIONS && gatk</token>\n+\n+ <!--Define sections that parameters could exist within.-->\n+ <template name="set_sections">\n+ #set global $sections = [\'\', \'optional.\', \'advanced.\', \'common.\', \'deprecated.\']\n+ </template>\n+\n+ <!--Reference genome handling-->\n+ <!--One template each for the different reference genome parameter names.-->\n+ <!--TODO: Can the reference parameters all be the same?-->\n+ <xml name="ref_sel">\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" type="select" label="Choose the source for the reference list">\n+ <option value="cached">Locally cached</option>\n+ <option value="history">History</option>\n+ <option value="no_ref" selected="true">Do not pass</option>\n+ </param>\n+ <when value="cached">\n+ <param name="reference_sequence" type="select" label="Reference" help="Reference sequence file." >\n+ <options from_data_table="all_fasta" >\n+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Reference sequence file." />\n+ </when>\n+ <when value="no_ref" />\n+ </conditional>\n+ </xml>\n+\n+ <template name="ref_opts">\n+ #for $sect in $sections\n+ #if $varExists($sect + "reference_source.reference_source_selector")\n+ #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"\n+ #if $getVar($sect + "reference_source.reference_source_selector") != "history"\n+ --reference $getVar($sect + "reference_source.reference_sequence.fields.path")\n+ #else\n+ --reference reference.fa\n+ #end if\n+ #end if\n+ #end if\n+ #end for\n+ </template>\n+\n+ <template name="picard_ref_opts">\n+ #for $sect in $sections\n+ #if $varExists($sect + "reference_source.reference_source_selector")\n+ #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"\n+ #if $getVar($sect + "reference_source.reference_source_selector") != "history"\n+ --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence.fields.path")\n+ #else\n+ --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence")\n+ #end if\n+ #end if\n+ #end if\n+ #end for\n+ </template>\n+\n+ <template name="picard_ref_opts_plain">\n+ #for $sect in $sections\n+ #if $varExists($sect + "reference_source.reference_source_selector")\n+ #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"\n+ #if $getVar($sect + "reference_'..b' <option value="STRICT" selected="true">STRICT</option>\n+ <option value="LENIENT" selected="false">LENIENT</option>\n+ <option value="SILENT" selected="false">SILENT</option>\n+ </param>\n+ <param argument="--VERBOSITY" type="select" optional="true" label="Verbosity" help="Control verbosity of logging." >\n+ <option value="ERROR" selected="false">ERROR</option>\n+ <option value="WARNING" selected="false">WARNING</option>\n+ <option value="INFO" selected="true">INFO</option>\n+ <option value="DEBUG" selected="false">DEBUG</option>\n+ </param>\n+ </section>\n+ </xml>\n+\n+ <!--Provides option to create gzipped output for VCF files-->\n+ <xml name="gzip_vcf_params">\n+ <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." />\n+ </xml>\n+\n+ <!--Output related Picard options-->\n+ <xml name="gzip_vcf_output_params">\n+ <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string}: vcf" from_work_dir="output.vcf" >\n+\t\t\t<filter>not gzipped_output</filter>\n+\t\t</data>\n+\t\t<data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: vcf_bgzip" from_work_dir="output.vcf.gz" >\n+\t\t\t<filter>gzipped_output</filter>\n+\t\t</data>\n+ </xml>\n+\n+\n+ <!--These are the same, other than the capitalization of output, so maybe a better way to do this.-->\n+ <template name="picard_vcf_output_opts">\n+ #if $gzipped_output\n+\t\t\t--OUTPUT output.vcf.gz\n+\t\t#else\n+\t\t\t--OUTPUT output.vcf\n+\t\t#end if\n+ </template>\n+\n+ <template name="vcf_output_opts">\n+ #if $gzipped_output\n+\t\t\t--output output.vcf.gz\n+\t\t#else\n+\t\t\t--output output.vcf\n+\t\t#end if\n+ </template>\n+\n+ <xml name="picard_output_params">\n+ <data format="txt" name="output_md5" label="${tool.name} on ${on_string}: md5sum(txt)" from_work_dir="output.bam.md5" >\n+\t\t\t<filter>picard_adv[\'CREATE_MD5_FILE\']</filter>\n+\t\t</data>\n+ </xml>\n+\n+\n+ <!--<template name="ref_opts">-->\n+ <!--#set $sections = [\'optional\',\'advanced\',\'common\',\'deprecated\',\'\']-->\n+ <!--#silent $sys.stderr.write("I WOULD LIKE TO SHOW THE SECTION VARIABLE: \'${sections}\'\\n")-->\n+ <!--#for $sect in $sections-->\n+ <!--#if $varExists(\'$sect.reference_source.reference_source_selector\')-->\n+ <!--#if $sect.reference_source.reference_source_selector != "no_ref"-->\n+ <!--#if $sect.reference_source.reference_source_selector != "history"-->\n+ <!----reference ${sect.reference_source.reference_sequence.fields.path}-->\n+ <!--#else-->\n+ <!----reference ${sect.reference_source.reference_sequence}-->\n+ <!--#end if-->\n+ <!--#end if-->\n+ <!--#end if-->\n+ <!--#end for-->\n+ <!--</template>-->\n+\n+\n+ <!--<template name="ref_opts_opt">-->\n+ <!--#if $optional.reference_source.reference_source_selector != "no_ref"-->\n+ <!--#if $optional.reference_source.reference_source_selector != "history"-->\n+ <!----reference ${optional.reference_source.reference_sequence.fields.path}-->\n+ <!--#else-->\n+ <!----reference ${optional.reference_source.reference_sequence}-->\n+ <!--#end if-->\n+ <!--#end if-->\n+ <!--</template>-->\n+\n+\n+ <!--Citations-->\n+ <xml name="citations">\n+ <citation type="doi">10.1101/gr.107524.110</citation>\n+ <citation type="doi">10.1038/ng.806</citation>\n+ <citation type="doi">10.1002/0471250953.bi1110s43</citation>\n+ <citation type="doi">10.1101/201178</citation>\n+ <yield />\n+ </xml>\n+\n+</macros>\n' |
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| diff -r 000000000000 -r f41a1e03538b test-data/Mutect2-in2.dict --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-in2.dict Wed Oct 30 15:33:59 2019 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r f41a1e03538b test-data/Mutect2-out1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out1.vcf Wed Oct 30 15:33:59 2019 -0400 |
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| b'@@ -0,0 +1,91 @@\n+##fileformat=VCFv4.2\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">\n+##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">\n+##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">\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 --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-diction'..b'=20,37;MFRL=197,291;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=64.46\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:30,20:0.466:50:10,8:13,12:13,17,7,13\n+K03455\t4376\t.\tC\tT\t.\t.\tDP=53;ECNT=15;MBQ=29,25;MFRL=231,244;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=80.90\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:28,24:0.446:52:8,10:16,12:9,19,11,13\n+K03455\t4397\t.\tT\tC\t.\t.\tDP=57;ECNT=15;MBQ=34,37;MFRL=291,247;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=66.78\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:32,19:0.381:51:9,8:17,9:15,17,9,10\n+K03455\t4416\t.\tC\tT\t.\t.\tDP=65;ECNT=21;MBQ=37,37;MFRL=270,310;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=33.57\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:54,11:0.193:65:21,4:31,4:22,32,6,5\n+K03455\t4418\t.\tA\tG\t.\t.\tDP=64;ECNT=21;MBQ=37,37;MFRL=287,229;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=6.89\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:61,3:0.066:64:24,3:35,0:26,35,1,2\n+K03455\t4421\t.\tT\tC\t.\t.\tDP=64;ECNT=21;MBQ=35,38;MFRL=259,291;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=140.93\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:28,36:0.574:64:15,13:10,21:11,17,16,20\n+K03455\t4424\t.\tT\tC\t.\t.\tDP=62;ECNT=21;MBQ=37,38;MFRL=251,291;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=104.68\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:32,29:0.498:61:14,9:12,17:12,20,14,15\n+K03455\t4430\t.\tT\tC\t.\t.\tDP=62;ECNT=21;MBQ=37,38;MFRL=284,265;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=3.90\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:60,2:0.051:62:24,2:31,0:25,35,1,1\n+K03455\t4439\t.\tA\tG\t.\t.\tDP=54;ECNT=21;MBQ=38,35;MFRL=291,241;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=18.97\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:48,6:0.115:54:21,2:24,4:21,27,2,4\n+K03455\t4442\t.\tAG\tGA\t.\t.\tDP=53;ECNT=21;MBQ=38,33;MFRL=290,209;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=18.54\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:45,7:0.159:52:18,2:23,5:19,26,3,4\n+K03455\t4443\t.\tG\tA\t.\t.\tDP=53;ECNT=21;MBQ=37,38;MFRL=282,297;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=75.44\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:26,22:0.454:48:12,9:10,10:10,16,11,11\n+K03455\t4448\t.\tC\tA\t.\t.\tDP=51;ECNT=21;MBQ=38,20;MFRL=290,126;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=9.07\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:47,3:0.062:50:18,0:25,2:20,27,1,2\n+K03455\t4449\t.\tC\tT\t.\t.\tDP=49;ECNT=21;MBQ=37,38;MFRL=209,323;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=90.60\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:25,24:0.511:49:11,10:13,13:11,14,11,13\n+K03455\t4460\t.\tT\tC\t.\t.\tDP=46;ECNT=21;MBQ=37,37;MFRL=284,329;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=18.65\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:40,6:0.159:46:15,2:22,3:20,20,2,4\n+K03455\t4465\t.\tT\tTGGCC\t.\t.\tDP=45;ECNT=21;MBQ=37,35;MFRL=310,176;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=26.99\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:35,8:0.170:43:12,6:21,1:17,18,4,4\n+K03455\t4466\t.\tA\tG,AGTG\t.\t.\tDP=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1/2:30,4,8:0.136,0.190:42:10,1,6:16,3,1:15,15,5,7\n+K03455\t4478\t.\tT\tC\t.\t.\tDP=33;ECNT=21;MBQ=37,33;MFRL=323,206;MMQ=60,60;MPOS=18;POPAF=7.30;TLOD=40.91\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:23,10:0.303:33:7,6:15,4:12,11,4,6\n+K03455\t4505\t.\tA\tG\t.\t.\tDP=19;ECNT=21;MBQ=39,38;MFRL=394,323;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=67.71\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:3,16:0.810:19:2,5:1,8:2,1,11,5\n+K03455\t4508\t.\tA\tT\t.\t.\tDP=17;ECNT=21;MBQ=39,35;MFRL=341,335;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=53.29\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:4,13:0.737:17:2,5:2,8:2,2,10,3\n+K03455\t4511\t.\tG\tA\t.\t.\tDP=17;ECNT=21;MBQ=37,36;MFRL=394,329;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=58.34\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:3,14:0.789:17:2,4:1,7:2,1,10,4\n+K03455\t4526\t.\tT\tC\t.\t.\tDP=13;ECNT=21;MBQ=0,36;MFRL=0,323;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=57.35\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,13:0.933:13:0,7:0,6:0,0,11,2\n+K03455\t4528\t.\tT\tTCA\t.\t.\tDP=13;ECNT=21;MBQ=38,37;MFRL=323,421;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=5.52\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:11,2:0.200:13:5,1:4,1:0|1:4528_T_TCA:4528:10,1,1,1\n+K03455\t4530\t.\tCTT\tC\t.\t.\tDP=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\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:10,2:0.213:12:5,1:4,1:0|1:4528_T_TCA:4528:9,1,1,1\n+K03455\t4532\t.\tT\tC\t.\t.\tDP=13;ECNT=21;MBQ=0,33;MFRL=0,323;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=39.42\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,11:0.926:11:0,7:0,2:0,0,11,0\n' |
| b |
| diff -r 000000000000 -r f41a1e03538b test-data/Mutect2-out2.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out2.vcf Wed Oct 30 15:33:59 2019 -0400 |
| b |
| b'@@ -0,0 +1,84 @@\n+##fileformat=VCFv4.2\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">\n+##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">\n+##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">\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-p'..b'K03455\t5131\t.\tG\tA\t.\t.\tDP=38;ECNT=27;MBQ=0,38;MFRL=0,205;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=23.77\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,8:0.932:8:0,1:0,6:0,0,1,7\n+K03455\t5133\t.\tT\tC\t.\t.\tDP=36;ECNT=27;MBQ=38,36;MFRL=293,216;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=31.26\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:27,9:0.268:36:2,0:23,8:0|1:5133_T_C:5133:2,25,0,9\n+K03455\t5137\t.\tGG\tAG,AA\t.\t.\tDP=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1/2:8,9,18:0.270,0.495:35:0,0,1:7,8,16:0,8,1,26\n+K03455\t5146\t.\tAGG\tA\t.\t.\tDP=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\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:24,9:0.286:33:1,0:22,9:0|1:5133_T_C:5133:1,23,0,9\n+K03455\t5147\t.\tG\tA\t.\t.\tDP=33;ECNT=27;MBQ=38,37;MFRL=181,343;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=66.04\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:7,17:0.694:24:0,0:6,13:0|1:5147_G_A:5147:0,7,1,16\n+K03455\t5153\t.\tGGTTT\tG\t.\t.\tDP=29;ECNT=27;MBQ=38,38;MFRL=296,216;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=32.02\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:20,9:0.323:29:0,0:19,9:0|1:5133_T_C:5133:0,20,0,9\n+K03455\t5155\t.\tT\tC\t.\t.\tDP=28;ECNT=27;MBQ=38,38;MFRL=169,331;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=49.64\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:6,13:0.669:19:0,0:6,12:0|1:5147_G_A:5147:0,6,0,13\n+K03455\t5156\t.\tT\tA\t.\t.\tDP=28;ECNT=27;MBQ=38,37;MFRL=315,181;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=16.29\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:14,5:0.283:19:0,0:14,5:0|1:5156_T_A:5156:0,14,0,5\n+K03455\t5157\t.\tT\tG\t.\t.\tDP=28;ECNT=27;MBQ=38,37;MFRL=181,331;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=49.65\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:5,13:0.703:18:0,0:5,13:0,5,0,13\n+K03455\t5169\t.\tC\tT\t.\t.\tDP=20;ECNT=27;MBQ=39,39;MFRL=296,170;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=20.02\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:14,6:0.318:20:0,0:14,6:0,14,0,6\n+K03455\t5175\t.\tA\tT\t.\t.\tDP=19;ECNT=27;MBQ=37,39;MFRL=203,299;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=34.23\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:10,9:0.476:19:0,0:9,9:0|1:5147_G_A:5147:0,10,0,9\n+K03455\t5177\t.\tG\tC\t.\t.\tDP=18;ECNT=27;MBQ=39,37;MFRL=299,216;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=25.72\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:11,7:0.400:18:0,0:10,7:0|1:5133_T_C:5133:0,11,0,7\n+K03455\t5179\t.\tCC\tAC,AA\t.\t.\tDP=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1/2:2,7,8:0.400,0.450:17:0,0,0:2,7,8:0,2,0,15\n+K03455\t5189\t.\tG\tA\t.\t.\tDP=18;ECNT=27;MBQ=39,39;MFRL=203,315;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=30.08\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:10,8:0.450:18:1,0:9,8:1,9,0,8\n+K03455\t5190\t.\tA\tG\t.\t.\tDP=18;ECNT=27;MBQ=39,20;MFRL=293,181;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=9.31\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:15,3:0.200:18:0,0:15,2:0|1:5156_T_A:5156:0,15,1,2\n+K03455\t5196\t.\tT\tC\t.\t.\tDP=18;ECNT=27;MBQ=39,37;MFRL=293,181;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=9.19\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:15,3:0.200:18:0,1:15,2:0,15,1,2\n+K03455\t5220\t.\tG\tA\t.\t.\tDP=16;ECNT=27;MBQ=38,38;MFRL=312,219;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=21.54\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:10,6:0.389:16:1,0:9,6:0|1:5220_G_A:5220:1,9,0,6\n+K03455\t5223\t.\tT\tA\t.\t.\tDP=16;ECNT=27;MBQ=37,39;MFRL=293,181;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=9.40\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:13,3:0.222:16:0,1:13,2:0|1:5223_T_A:5223:0,13,1,2\n+K03455\t5230\t.\tT\tC\t.\t.\tDP=16;ECNT=27;MBQ=38,39;MFRL=293,181;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=9.40\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:13,3:0.222:16:0,1:12,2:0|1:5223_T_A:5223:0,13,1,2\n+K03455\t5233\t.\tG\tA\t.\t.\tDP=12;ECNT=27;MBQ=38,38;MFRL=293,216;MMQ=60,60;MPOS=11;POPAF=7.30;TLOD=18.49\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:7,5:0.429:12:0,0:6,5:0|1:5220_G_A:5220:1,6,0,5\n+K03455\t5236\t.\tA\tG\t.\t.\tDP=12;ECNT=27;MBQ=37,38;MFRL=216,256;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=22.57\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:5,6:0.539:11:0,1:5,5:0,5,1,5\n+K03455\t5240\t.\tC\tT\t.\t.\tDP=11;ECNT=27;MBQ=37,37;MFRL=219,162;MMQ=60,60;MPOS=-1;POPAF=7.30;TLOD=9.66\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:8,3:0.308:11:0,0:7,3:1,7,0,3\n' |
| b |
| diff -r 000000000000 -r f41a1e03538b test-data/Mutect2-out3.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out3.vcf Wed Oct 30 15:33:59 2019 -0400 |
| b |
| b'@@ -0,0 +1,66 @@\n+##fileformat=VCFv4.2\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">\n+##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">\n+##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">\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 --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-ac'..b'=6,7;RU=A;STR;TLOD=1256.09\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:13,560:0.982:573:6,264:7,260:8,5,299,261\n+K03455\t2849\t.\tA\tAG\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:577,8:0.012:585:285,2:261,5:309,268,4,4\n+K03455\t2872\t.\tT\tA\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:559,25:0.023:584:222,1:230,0:259,300,25,0\n+K03455\t2874\t.\tC\tT\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:1,595:0.997:596:0,262:0,249:1,0,292,303\n+K03455\t2882\t.\tG\tT\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:1,568:0.997:569:1,254:0,252:1,0,287,281\n+K03455\t2889\t.\tG\tA\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:552,7:0.016:559:244,4:256,3:282,270,6,1\n+K03455\t2891\t.\tA\tG\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:543,9:0.013:552:237,4:257,4:276,267,5,4\n+K03455\t2894\t.\tT\tC\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,551:0.998:551:0,236:0,249:0,0,280,271\n+K03455\t2906\t.\tC\tT\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,495:0.998:495:0,225:0,254:0|1:2906_C_T:2906:0,0,235,260\n+K03455\t2913\t.\tG\tA\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,492:0.998:492:0,224:0,251:0|1:2906_C_T:2906:0,0,234,258\n+K03455\t2987\t.\tC\tT\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,219:0.995:219:0,99:0,103:0,0,86,133\n+K03455\t2992\t.\tT\tG\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:179,9:0.043:188:74,2:77,0:74,105,9,0\n+K03455\t3016\t.\tC\tA\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:88,7:0.081:95:24,1:34,0:61,27,7,0\n+K03455\t3020\t.\tA\tG\t.\t.\tBQHIST=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,90:0.989:90:0,32:0,43:0,0,65,25\n' |
| b |
| diff -r 000000000000 -r f41a1e03538b test-data/Mutect2-out4.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out4.vcf Wed Oct 30 15:33:59 2019 -0400 |
| b |
| b'@@ -0,0 +1,75 @@\n+##fileformat=VCFv4.2\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">\n+##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">\n+##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">\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 --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 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|
| b |
| diff -r 000000000000 -r f41a1e03538b test-data/Mutect2-out5-1.tabular --- /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 |
| b |
| b'@@ -0,0 +1,9721 @@\n+#track 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0\n+K03455\t9603\t9604\tstate\t0.00000\n+K03455\t9604\t9605\tstate\t0.00000\n+K03455\t9605\t9606\tstate\t0.00000\n+K03455\t9606\t9607\tstate\t0.00000\n+K03455\t9607\t9608\tstate\t0.00000\n+K03455\t9608\t9609\tstate\t0.00000\n+K03455\t9609\t9610\tstate\t0.00000\n+K03455\t9610\t9611\tstate\t0.00000\n+K03455\t9611\t9612\tstate\t0.00000\n+K03455\t9612\t9613\tstate\t0.00000\n+K03455\t9613\t9614\tstate\t0.00000\n+K03455\t9614\t9615\tstate\t0.00000\n+K03455\t9615\t9616\tstate\t0.00000\n+K03455\t9616\t9617\tstate\t0.00000\n+K03455\t9617\t9618\tstate\t0.00000\n+K03455\t9618\t9619\tstate\t0.00000\n+K03455\t9619\t9620\tstate\t0.00000\n+K03455\t9620\t9621\tstate\t0.00000\n+K03455\t9621\t9622\tstate\t0.00000\n+K03455\t9622\t9623\tstate\t0.00000\n+K03455\t9623\t9624\tstate\t0.00000\n+K03455\t9624\t9625\tstate\t0.00000\n+K03455\t9625\t9626\tstate\t0.00000\n+K03455\t9626\t9627\tstate\t0.00000\n+K03455\t9627\t9628\tstate\t0.00000\n+K03455\t9628\t9629\tstate\t0.00000\n+K03455\t9629\t9630\tstate\t0.00000\n+K03455\t9630\t9631\tstate\t0.00000\n+K03455\t9631\t9632\tstate\t0.00000\n+K03455\t9632\t9633\tstate\t0.00000\n+K03455\t9633\t9634\tstate\t0.00000\n+K03455\t9634\t9635\tstate\t0.00000\n+K03455\t9635\t9636\tstate\t0.00000\n+K03455\t9636\t9637\tstate\t0.00000\n+K03455\t9637\t9638\tstate\t0.00000\n+K03455\t9638\t9639\tstate\t0.00000\n+K03455\t9639\t9640\tstate\t0.00000\n+K03455\t9640\t9641\tstate\t0.00000\n+K03455\t9641\t9642\tstate\t0.00000\n+K03455\t9642\t9643\tstate\t0.00000\n+K03455\t9643\t9644\tstate\t0.00000\n+K03455\t9644\t9645\tstate\t0.00000\n+K03455\t9645\t9646\tstate\t0.00000\n+K03455\t9646\t9647\tstate\t0.00000\n+K03455\t9647\t9648\tstate\t0.00000\n+K03455\t9648\t9649\tstate\t0.00000\n+K03455\t9649\t9650\tstate\t0.00000\n+K03455\t9650\t9651\tstate\t0.00000\n+K03455\t9651\t9652\tstate\t0.00000\n+K03455\t9652\t9653\tstate\t0.00000\n+K03455\t9653\t9654\tstate\t0.00000\n+K03455\t9654\t9655\tstate\t0.00000\n+K03455\t9655\t9656\tstate\t0.00000\n+K03455\t9656\t9657\tstate\t0.00000\n+K03455\t9657\t9658\tstate\t0.00000\n+K03455\t9658\t9659\tstate\t0.00000\n+K03455\t9659\t9660\tstate\t0.00000\n+K03455\t9660\t9661\tstate\t0.00000\n+K03455\t9661\t9662\tstate\t0.00000\n+K03455\t9662\t9663\tstate\t0.00000\n+K03455\t9663\t9664\tstate\t0.00000\n+K03455\t9664\t9665\tstate\t0.00000\n+K03455\t9665\t9666\tstate\t0.00000\n+K03455\t9666\t9667\tstate\t0.00000\n+K03455\t9667\t9668\tstate\t0.00000\n+K03455\t9668\t9669\tstate\t0.00000\n+K03455\t9669\t9670\tstate\t0.00000\n+K03455\t9670\t9671\tstate\t0.00000\n+K03455\t9671\t9672\tstate\t0.00000\n+K03455\t9672\t9673\tstate\t0.00000\n+K03455\t9673\t9674\tstate\t0.00000\n+K03455\t9674\t9675\tstate\t0.00000\n+K03455\t9675\t9676\tstate\t0.00000\n+K03455\t9676\t9677\tstate\t0.00000\n+K03455\t9677\t9678\tstate\t0.00000\n+K03455\t9678\t9679\tstate\t0.00000\n+K03455\t9679\t9680\tstate\t0.00000\n+K03455\t9680\t9681\tstate\t0.00000\n+K03455\t9681\t9682\tstate\t0.00000\n+K03455\t9682\t9683\tstate\t0.00000\n+K03455\t9683\t9684\tstate\t0.00000\n+K03455\t9684\t9685\tstate\t0.00000\n+K03455\t9685\t9686\tstate\t0.00000\n+K03455\t9686\t9687\tstate\t0.00000\n+K03455\t9687\t9688\tstate\t0.00000\n+K03455\t9688\t9689\tstate\t0.00000\n+K03455\t9689\t9690\tstate\t0.00000\n+K03455\t9690\t9691\tstate\t0.00000\n+K03455\t9691\t9692\tstate\t0.00000\n+K03455\t9692\t9693\tstate\t0.00000\n+K03455\t9693\t9694\tstate\t0.00000\n+K03455\t9694\t9695\tstate\t0.00000\n+K03455\t9695\t9696\tstate\t0.00000\n+K03455\t9696\t9697\tstate\t0.00000\n+K03455\t9697\t9698\tstate\t0.00000\n+K03455\t9698\t9699\tstate\t0.00000\n+K03455\t9699\t9700\tstate\t0.00000\n+K03455\t9700\t9701\tstate\t0.00000\n+K03455\t9701\t9702\tstate\t0.00000\n+K03455\t9702\t9703\tstate\t0.00000\n+K03455\t9703\t9704\tstate\t0.00000\n+K03455\t9704\t9705\tstate\t0.00000\n+K03455\t9705\t9706\tstate\t0.00000\n+K03455\t9706\t9707\tstate\t0.00000\n+K03455\t9707\t9708\tstate\t0.00000\n+K03455\t9708\t9709\tstate\t0.00000\n+K03455\t9709\t9710\tstate\t0.00000\n+K03455\t9710\t9711\tstate\t0.00000\n+K03455\t9711\t9712\tstate\t0.00000\n+K03455\t9712\t9713\tstate\t0.00000\n+K03455\t9713\t9714\tstate\t0.00000\n+K03455\t9714\t9715\tstate\t0.00000\n+K03455\t9715\t9716\tstate\t0.00000\n+K03455\t9716\t9717\tstate\t0.00000\n+K03455\t9717\t9718\tstate\t0.00000\n+K03455\t9718\t9719\tstate\t0.00000\n' |
| b |
| diff -r 000000000000 -r f41a1e03538b test-data/Mutect2-out5-2.tabular --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r f41a1e03538b test-data/Mutect2-out5.bam |
| b |
| Binary file test-data/Mutect2-out5.bam has changed |
| b |
| diff -r 000000000000 -r f41a1e03538b test-data/Mutect2-out5.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out5.vcf Wed Oct 30 15:33:59 2019 -0400 |
| b |
| b'@@ -0,0 +1,93 @@\n+##fileformat=VCFv4.2\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">\n+##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">\n+##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">\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 --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-ru'..b'\tACC\t.\t.\tDP=45;ECNT=41;MBQ=37,34;MFRL=232,211;MMQ=60,60;MPOS=-2147483648;POPAF=7.30;TLOD=61.64\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:9,24:0.731:33:4,13:4,9:5,4,14,10\n+K03455\t2248\t.\tA\tG\t.\t.\tDP=46;ECNT=41;MBQ=20,38;MFRL=197,247;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=185.50\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t1|0:6,40:0.884:46:3,21:3,16:1|0:2200_ACTC_A:2200:4,2,27,13\n+K03455\t2250\t.\tT\tC\t.\t.\tDP=46;ECNT=41;MBQ=38,37;MFRL=247,197;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=15.87\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:40,6:0.116:46:23,3:16,3:0|1:2200_ACTC_A:2200:27,13,4,2\n+K03455\t2258\t.\tGG\tAA\t.\t.\tDP=48;ECNT=41;MBQ=38,39;MFRL=241,235;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=163.72\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:7,41:0.843:48:3,23:3,17:0|1:2258_GG_AA:2258:6,1,27,14\n+K03455\t2259\t.\tG\tA\t.\t.\tDP=48;ECNT=41;MBQ=0,37;MFRL=0,242;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=17.05\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t1|0:0,14:0.919:14:0,5:0,8:1|0:2258_GG_AA:2258:0,0,10,4\n+K03455\t2282\t.\tC\tT\t.\t.\tDP=62;ECNT=41;MBQ=35,20;MFRL=241,182;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=12.25\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:57,5:0.075:62:24,2:24,2:32,25,3,2\n+K03455\t2285\t.\tC\tT\t.\t.\tDP=65;ECNT=41;MBQ=28,38;MFRL=239,209;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=30.08\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:54,10:0.164:64:24,4:21,4:30,24,7,3\n+K03455\t2287\t.\tCA\tAT\t.\t.\tDP=68;ECNT=41;MBQ=33,37;MFRL=232,285;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=17.29\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:61,7:0.128:68:26,1:25,2:33,28,4,3\n+K03455\t2300\t.\tG\tA\t.\t.\tDP=67;ECNT=41;MBQ=31,32;MFRL=219,236;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=209.86\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:16,49:0.754:65:5,20:7,22:8,8,26,23\n+K03455\t2303\t.\tGCA\tG\t.\t.\tDP=65;ECNT=41;MBQ=36,31;MFRL=221,241;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=170.03\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:19,45:0.695:64:4,18:11,20:9,10,25,20\n+K03455\t2304\t.\tCAA\tGTG\t.\t.\tDP=65;ECNT=41;MBQ=33,20;MFRL=219,235;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=3.43\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:16,19:0.471:35:6,4:9,12:8,8,10,9\n+K03455\t2306\t.\tA\tATG,G\t.\t.\tDP=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\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1/2:7,48,9:0.738,0.173:64:4,20,2:3,23,5:4,3,30,27\n+K03455\t2315\t.\tA\tG\t.\t.\tDP=63;ECNT=41;MBQ=37,38;MFRL=219,244;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=74.04\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:42,20:0.358:62:18,6:17,14:0|1:2315_A_G:2315:21,21,11,9\n+K03455\t2321\t.\tA\tC\t.\t.\tDP=60;ECNT=41;MBQ=33,37;MFRL=212,244;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=74.63\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:39,20:0.377:59:18,6:18,14:0|1:2315_A_G:2315:19,20,11,9\n+K03455\t2349\t.\tT\tC\t.\t.\tDP=53;ECNT=9;MBQ=34,35;MFRL=234,259;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=21.63\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:46,7:0.160:53:18,3:22,4:24,22,3,4\n+K03455\t2360\t.\tG\tA\t.\t.\tDP=48;ECNT=9;MBQ=37,34;MFRL=235,232;MMQ=60,60;MPOS=43;POPAF=7.30;TLOD=20.61\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:41,7:0.175:48:16,3:22,3:22,19,3,4\n+K03455\t2362\t.\tG\tA\t.\t.\tDP=48;ECNT=9;MBQ=0,37;MFRL=0,234;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=178.56\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,46:0.978:46:0,20:0,24:0,0,23,23\n+K03455\t2372\t.\tA\tG\t.\t.\tDP=43;ECNT=9;MBQ=37,36;MFRL=237,227;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=22.64\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:36,7:0.192:43:8,2:17,4:19,17,3,4\n+K03455\t2374\t.\tG\tA\t.\t.\tDP=34;ECNT=9;MBQ=37,37;MFRL=227,255;MMQ=60,60;MPOS=9;POPAF=7.30;TLOD=4.41\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:31,3:0.102:34:8,0:18,2:11,20,2,1\n+K03455\t2423\t.\tA\tG\t.\t.\tDP=14;ECNT=9;MBQ=34,36;MFRL=248,221;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=5.14\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:12,2:0.187:14:3,0:8,2:0,12,0,2\n+K03455\t2436\t.\tA\tG\t.\t.\tDP=4;ECNT=9;MBQ=16,33;MFRL=255,255;MMQ=60,60;MPOS=4;POPAF=7.30;TLOD=12.21\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:1,3:0.671:4:0,0:0,3:0,1,0,3\n+K03455\t2438\t.\tA\tG\t.\t.\tDP=4;ECNT=9;MBQ=24,33;MFRL=255,255;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=7.53\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:2,2:0.502:4:0,0:1,2:0|1:2438_A_G:2438:0,2,0,2\n+K03455\t2440\t.\tT\tC\t.\t.\tDP=4;ECNT=9;MBQ=0,31;MFRL=255,255;MMQ=60,60;MPOS=1;POPAF=7.30;TLOD=7.53\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:2,2:0.502:4:0,0:0,2:0|1:2438_A_G:2438:0,2,0,2\n' |
| b |
| diff -r 000000000000 -r f41a1e03538b test-data/reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fa Wed Oct 30 15:33:59 2019 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>K03455\n+TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCA'..b'CAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA\n' |
| b |
| diff -r 000000000000 -r f41a1e03538b tool-data/all_fasta.loc.sample --- /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 |
| b |
| @@ -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. +# |
| b |
| diff -r 000000000000 -r f41a1e03538b tool-data/tool_data_table_conf.xml.sample --- /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 |
| b |
| @@ -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> |