| Next changeset 1:b040adcfeefd (2022-01-04) |
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Commit message:
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" |
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added:
FilterMutectCalls.xml Mutect2.xml macros.xml macros_filtermutectcalls.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-out1.vcf.gz test-data/Mutect2-out1.vcf.stats 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/Mutect2-out6.vcf test-data/Mutect2-out6.vcf_bgzip test-data/Mutect2-out6.vcf_bgzip.stats test-data/all_fasta.loc test-data/cached_locally/all_fasta.loc test-data/cached_locally/cached_reference.fa test-data/chr20.fa test-data/filtered_Mutect2-out1.vcf test-data/filtered_Mutect2-out1_stats.tsv test-data/filtered_Mutect2-out6.vcf test-data/filtered_Mutect2-out6.vcf_bgzip test-data/filtered_Mutect2-out6_stats.tsv test-data/normal.bam test-data/reference.fa test-data/tumor.bam tool-data/all_fasta.loc.sample tool-data/tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r c51c08cc9fcc FilterMutectCalls.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FilterMutectCalls.xml Wed Dec 29 01:36:41 2021 +0000 |
| [ |
| b'@@ -0,0 +1,513 @@\n+<tool id="filtermutectcalls" name="gatk4 FilterMutectCalls" version="@WRAPPER_VERSION@" profile="18.05">\n+ <description>Filter variants in a GATK4 Mutect2 VCF callset</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+ #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($reference_source.reference_source_selector) == \'cached\'\n+ ln -s \'$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($input_options.input_options_selector) == \'vcf\'\n+ ln -s \'$input_options.unfiltered_vcf_input\' input.vcf &&\n+ ln -s \'$gatk_vcf_stats\' input.vcf.stats &&\n+ #else if str($input_options.input_options_selector) == \'vcf_bgzip\'\n+ ln -s \'$input_options.unfiltered_vcf_input\' input.vcf.gz &&\n+ ln -s \'$gatk_vcf_stats\' input.vcf.gz.stats &&\n+ gatk IndexFeatureFile --input input.vcf.gz &&\n+ #end if\n+\n+ gatk FilterMutectCalls --QUIET $ref_flag\n+ --variant\n+ #if str($input_options.input_options_selector) == \'vcf\'\n+ input.vcf\n+ #else if str($input_options.input_options_selector) == \'vcf_bgzip\'\n+ input.vcf.gz\n+ #end if\n+ --output\n+ #if str($input_options.input_options_selector) == \'vcf\'\n+ filtered.vcf\n+ #else if str($input_options.input_options_selector) == \'vcf_bgzip\'\n+ filtered.vcf.gz\n+ #end if\n+ ]]>\n+ </command>\n+ <inputs>\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" selected="true">History</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+ </conditional>\n+ <conditional name="input_options">\n+ <param name="input_options_selector" type="select" label="Format of input variant dataset">\n+ <option value="vcf" selected="true">vcf</option>\n+ <option value="vcf_bgzip">vcf_bgzip</option>\n+ </param>\n+ <when value="vcf">\n+ <param name="unfiltered_vcf_input" type="data" format="vcf" label="vcf input file." />\n+ </when>\n+ <when value="vcf_bgzip">\n+ <param name="unfiltered_vcf_input" type="data" format="vcf_bgzip" label="vcf_bgzip input file" />\n+ </when>\n+ </conditional>\n+ <param format='..b'mapping quality to keep (inclusive) Default value: null.\n+ \n+ --minimum-mapping-quality:Integer\n+ Minimum mapping quality to keep (inclusive) Default value: 10.\n+ \n+ Valid only if "MateDistantReadFilter" is specified:\n+ --mate-too-distant-length:Integer\n+ Minimum start location difference at which mapped mates are considered distant Default\n+ value: 1000.\n+ \n+ Valid only if "OverclippedReadFilter" is specified:\n+ --dont-require-soft-clips-both-ends:Boolean\n+ Allow a read to be filtered out based on having only 1 soft-clipped block. By default,\n+ both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped\n+ block Default value: false. Possible values: {true, false}\n+ \n+ --filter-too-short:Integer Minimum number of aligned bases Default value: 30.\n+ \n+ Valid only if "PlatformReadFilter" is specified:\n+ --platform-filter-name:String Platform attribute (PL) to match This argument must be specified at least once. Required.\n+ \n+ Valid only if "PlatformUnitReadFilter" is specified:\n+ --black-listed-lanes:String Platform unit (PU) to filter out This argument must be specified at least once. Required.\n+ \n+ Valid only if "ReadGroupBlackListReadFilter" is specified:\n+ --read-group-black-list:StringA read group filter expression in the form "attribute:value", where "attribute" is a two\n+ character read group attribute such as "RG" or "PU". This argument must be specified at\n+ least once. Required.\n+ \n+ Valid only if "ReadGroupReadFilter" is specified:\n+ --keep-read-group:String The name of the read group to keep Required.\n+ \n+ Valid only if "ReadLengthReadFilter" is specified:\n+ --max-read-length:Integer Keep only reads with length at most equal to the specified value Required.\n+ \n+ --min-read-length:Integer Keep only reads with length at least equal to the specified value Default value: 1.\n+ \n+ Valid only if "ReadNameReadFilter" is specified:\n+ --read-name:String Keep only reads with this read name Required.\n+ \n+ Valid only if "ReadStrandFilter" is specified:\n+ --keep-reverse-strand-only:Boolean\n+ Keep only reads on the reverse strand Required. Possible values: {true, false}\n+ \n+ Valid only if "SampleReadFilter" is specified:\n+ --sample,-sample:String The name of the sample(s) to keep, filtering out all others This argument must be\n+ specified at least once. Required.\n+ \n+ Valid only if "SoftClippedReadFilter" is specified:\n+ --invert-soft-clip-ratio-filter:Boolean\n+ Inverts the results from this filter, causing all variants that would pass to fail and\n+ visa-versa. Default value: false. Possible values: {true, false}\n+ \n+ --soft-clipped-leading-trailing-ratio:Double\n+ Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases\n+ in read for read to be filtered. Default value: null. Cannot be used in conjuction with\n+ argument(s) minimumSoftClippedRatio\n+ \n+ --soft-clipped-ratio-threshold:Double\n+ Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in\n+ read for read to be filtered. Default value: null. Cannot be used in conjuction with\n+ argument(s) minimumLeadingTrailingSoftClippedRatio\n+\n+\n+]]></help>\n+ <citations>\n+ <expand macro="citations"/>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r c51c08cc9fcc Mutect2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Mutect2.xml Wed Dec 29 01:36:41 2021 +0000 |
| [ |
| b'@@ -0,0 +1,815 @@\n+<tool id="mutect2" name="gatk4 Mutect2" version="@WRAPPER_VERSION@" 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=$pre_gatk_excl_ints_chth#\n+ #include source=$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($reference_source.reference_source_selector) == \'cached\'\n+ ln -s \'$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($mode.mode_parameters) == \'tumor_only\'\n+ ln -s $mode.tumor tumor.bam &&\n+ ln -s $mode.tumor.metadata.bam_index tumor.bam.bai &&\n+ #else\n+ ln -s $mode.tumor tumor.bam &&\n+ ln -s $mode.tumor.metadata.bam_index tumor.bam.bai &&\n+ ln -s $mode.normal normal.bam &&\n+ ln -s $mode.normal.metadata.bam_index normal.bam.bai &&\n+ #end if\n+\n+ #if str($outputs.output_parameters) == \'yes\'\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+ gatk GetSampleName --input="tumor.bam" --output="samplename.txt" &&\n+ sample=`cat samplename.txt | sed \'s/"//g\'` &&\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.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 if\n+\n+ gatk Mutect2 --QUIET $ref_flag --tumor-sample "\\$sample"\n+\n+ #if str($mode.mode_parameters) == \'tumor_only\'\n+ --input tumor.bam\n+ #else\n+ --input tumor.bam\n+ --input normal.bam\n+ #end if\n+'..b'll emit the variant to the callset 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' |
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| diff -r 000000000000 -r c51c08cc9fcc macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 29 01:36:41 2021 +0000 |
| [ |
| b'@@ -0,0 +1,673 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <token name="@VERSION@">4.1.7.0</token>\n+ <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</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+ <!--Define sections that parameters could exist within.-->\n+ <template name="set_sections">\n+ #set global $sections = [\'\', \'optional.\', \'advanced.\', \'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_source.reference_source_selector") != "history"\n+ --REFERENCE $getVar($sect + "reference_source.reference_sequence.fields.path")\n+ #else\n+ --REFERENCE $ge'..b'value="WARNING" selected="false">WARNING</option>\n+ <option value="INFO" selected="true">INFO</option>\n+ <option value="DEBUG" selected="false">DEBUG</option>\n+ </param>\n+ </section>\n+ </xml>\n+\n+ <!--Provides option to create gzipped output for VCF files-->\n+ <xml name="gzip_vcf_params">\n+ <param name="gzipped_output" type="boolean" checked="true" label="GZIP Output?" help="If you would like gzipped output, check this box. In general, it would be preferable to do this, unless your downstream tool does not support handling of gzipped files." />\n+ </xml>\n+\n+ <!--Output related Picard options-->\n+ <xml name="gzip_vcf_output_params">\n+ <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string}: vcf" from_work_dir="output.vcf" >\n+ <filter>not gzipped_output</filter>\n+ </data>\n+ <data format="tabular" name="output_vcf_stats" label="gatk vcf stats" from_work_dir="output.vcf.stats" >\n+ <filter>not gzipped_output</filter>\n+ </data>\n+ <data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: vcf_bgzip" from_work_dir="output.vcf.gz" >\n+ <filter>gzipped_output</filter>\n+ </data>\n+ <data format="tabular" name="output_vcf_bgzip_stats" label="gatk vcf stats" from_work_dir="output.vcf.gz.stats" >\n+ <filter>gzipped_output</filter>\n+ </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+ --OUTPUT output.vcf.gz\n+ #else\n+ --OUTPUT output.vcf\n+ #end if\n+ </template>\n+\n+ <template name="vcf_output_opts">\n+ #if $gzipped_output\n+ --output output.vcf.gz\n+ #else\n+ --output output.vcf\n+ #end if\n+ </template>\n+\n+ <xml name="picard_output_params">\n+ <data format="txt" name="output_md5" label="${tool.name} on ${on_string}: md5sum(txt)" from_work_dir="output.bam.md5" >\n+ <filter>picard_adv[\'CREATE_MD5_FILE\']</filter>\n+ </data>\n+ </xml>\n+\n+\n+ <!--<template name="ref_opts">-->\n+ <!--#set $sections = [\'optional\',\'advanced\',\'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 c51c08cc9fcc macros_filtermutectcalls.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_filtermutectcalls.xml Wed Dec 29 01:36:41 2021 +0000 |
| [ |
| b'@@ -0,0 +1,592 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <token name="@VERSION@">4.1.7.0</token>\n+ <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</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+ <!--Define sections that parameters could exist within.-->\n+ <template name="set_sections">\n+ #set global $sections = [\'\', \'optional.\', \'advanced.\', \'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_source.reference_source_selector") != "history"\n+ --REFERENCE $getVar($sect + "reference_source.reference_sequence.fields.path")\n+ #else\n+ --REFERENCE $ge'..b'f file handles needed to sort the file, and increases the amount of RAM needed." />\n+ <param argument="--TMP_DIR" type="text" optional="true" label="Tmp Dir" help="One or more directories with space available to be used by this program for temporary storage of working files. Keep in mind, you must be able to access this directory from either your user, or from the Galaxy user, depending on your configuration." />\n+ <param argument="--USE_JDK_DEFLATER" truevalue="--USE_JDK_DEFLATER" falsevalue="" type="boolean" optional="true" checked="false" label="Use Jdk Deflater" help="Use the JDK Deflater instead of the Intel Deflater for writing compressed output" />\n+ <param argument="--USE_JDK_INFLATER" truevalue="--USE_JDK_INFLATER" falsevalue="" type="boolean" optional="true" checked="false" label="Use Jdk Inflater" help="Use the JDK Inflater instead of the Intel Inflater for reading compressed input" />\n+ <param argument="--VALIDATION_STRINGENCY" type="select" optional="true" label="Validation Stringency" help="Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded." >\n+ <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 ${on_string}: vcf" from_work_dir="output.vcf" >\n+ <filter>not gzipped_output</filter>\n+ </data>\n+ <data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: vcf_bgzip" from_work_dir="output.vcf.gz" >\n+ <filter>gzipped_output</filter>\n+ </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+ --OUTPUT output.vcf.gz\n+ #else\n+ --OUTPUT output.vcf\n+ #end if\n+ </template>\n+\n+ <template name="vcf_output_opts">\n+ #if $gzipped_output\n+ --output output.vcf.gz\n+ #else\n+ --output output.vcf\n+ #end if\n+ </template>\n+\n+ <xml name="picard_output_params">\n+ <data format="txt" name="output_md5" label="${tool.name} on ${on_string}: md5sum(txt)" from_work_dir="output.bam.md5" >\n+ <filter>picard_adv[\'CREATE_MD5_FILE\']</filter>\n+ </data>\n+ </xml>\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\\ No newline at end of file\n' |
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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 c51c08cc9fcc test-data/Mutect2-out1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out1.vcf Wed Dec 29 01:36:41 2021 +0000 |
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| 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; will always be heterozygous and is not intended to describe called alleles">\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 tumor.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 --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 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --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 --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padd'..b'6\t.\tC\tT\t.\t.\tAS_SB_TABLE=22,34|6,6;DP=68;ECNT=21;MBQ=37,37;MFRL=270,305;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=37.06\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:56,12:0.197:68:20,5:33,4:22,34,6,6\n+K03455\t4418\t.\tA\tG\t.\t.\tAS_SB_TABLE=26,38|1,2;DP=67;ECNT=21;MBQ=37,37;MFRL=284,229;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=6.77\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:64,3:0.062:67:24,3:35,0:26,38,1,2\n+K03455\t4421\t.\tT\tC\t.\t.\tAS_SB_TABLE=11,20|16,20;DP=67;ECNT=21;MBQ=34,38;MFRL=263,291;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=142.09\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:31,36:0.538:67:16,14:12,21:11,20,16,20\n+K03455\t4424\t.\tT\tC\t.\t.\tAS_SB_TABLE=13,24|13,15;DP=65;ECNT=21;MBQ=37,38;MFRL=254,295;MMQ=60,60;MPOS=35;POPAF=7.30;TLOD=102.79\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:37,28:0.444:65:15,9:15,17:13,24,13,15\n+K03455\t4430\t.\tT\tC\t.\t.\tAS_SB_TABLE=25,37|1,2;DP=65;ECNT=21;MBQ=37,36;MFRL=280,300;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=7.02\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:62,3:0.063:65:26,2:32,1:25,37,1,2\n+K03455\t4439\t.\tA\tG\t.\t.\tAS_SB_TABLE=22,31|3,4;DP=60;ECNT=21;MBQ=38,35;MFRL=287,210;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=21.26\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:53,7:0.121:60:23,3:26,4:22,31,3,4\n+K03455\t4442\t.\tAG\tGA\t.\t.\tAS_SB_TABLE=21,30|3,4;DP=59;ECNT=21;MBQ=37,33;MFRL=287,209;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=18.12\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:51,7:0.142:58:20,2:25,5:21,30,3,4\n+K03455\t4443\t.\tG\tA\t.\t.\tAS_SB_TABLE=12,19|11,12;DP=59;ECNT=21;MBQ=35,38;MFRL=276,291;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=78.51\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:31,23:0.421:54:14,10:13,10:12,19,11,12\n+K03455\t4448\t.\tC\tA\t.\t.\tAS_SB_TABLE=22,31|1,2;DP=57;ECNT=21;MBQ=37,20;MFRL=287,126;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=8.91\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:53,3:0.055:56:21,0:27,2:22,31,1,2\n+K03455\t4449\t.\tC\tT\t.\t.\tAS_SB_TABLE=13,16|11,15;DP=55;ECNT=21;MBQ=37,38;MFRL=209,322;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=97.76\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:29,26:0.491:55:11,12:16,13:13,16,11,15\n+K03455\t4460\t.\tT\tC\t.\t.\tAS_SB_TABLE=22,22|2,5;DP=51;ECNT=21;MBQ=37,37;MFRL=279,321;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=22.02\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:44,7:0.163:51:17,3:24,3:22,22,2,5\n+K03455\t4465\t.\tT\tTGGCC\t.\t.\tAS_SB_TABLE=19,20|4,4;DP=50;ECNT=21;MBQ=37,35;MFRL=290,176;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=26.66\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:39,8:0.155:47:14,6:22,1:19,20,4,4\n+K03455\t4466\t.\tA\tG,AGTG\t.\t.\tAS_SB_TABLE=16,17|2,3|4,4;DP=49;ECNT=21;MBQ=37,38,37;MFRL=310,207,176;MMQ=60,60,60;MPOS=20,25;POPAF=7.30,7.30;TLOD=15.50,28.09\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1/2:33,5,8:0.154,0.179:46:12,1,6:16,4,1:16,17,6,7\n+K03455\t4478\t.\tT\tC\t.\t.\tAS_SB_TABLE=12,13|5,6;DP=36;ECNT=21;MBQ=37,32;MFRL=323,205;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=44.55\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:25,11:0.306:36:9,6:15,4:12,13,5,6\n+K03455\t4505\t.\tA\tG\t.\t.\tAS_SB_TABLE=2,1|11,6;DP=20;ECNT=21;MBQ=39,37;MFRL=394,323;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=72.12\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:3,17:0.818:20:2,6:1,8:2,1,11,6\n+K03455\t4508\t.\tA\tT\t.\t.\tAS_SB_TABLE=2,3|10,3;DP=18;ECNT=21;MBQ=39,35;MFRL=287,335;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=52.71\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:5,13:0.700:18:3,5:2,8:2,3,10,3\n+K03455\t4511\t.\tG\tA\t.\t.\tAS_SB_TABLE=2,1|10,5;DP=18;ECNT=21;MBQ=37,35;MFRL=394,323;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=62.74\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:3,15:0.800:18:2,5:1,7:2,1,10,5\n+K03455\t4526\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|11,2;DP=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.\tAS_SB_TABLE=10,1|1,1;DP=13;ECNT=21;MBQ=38,37;MFRL=323,421;MMQ=60,60;MPOS=38;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.\tAS_SB_TABLE=9,1|1,1;DP=13;ECNT=21;MBQ=35,38;MFRL=323,421;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=4,2;RU=T;STR;TLOD=6.12\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.\tAS_SB_TABLE=0,0|11,0;DP=13;ECNT=21;MBQ=0,27;MFRL=0,323;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=39.42\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,11:0.926:11:0,6:0,2:0,0,11,0\n' 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| diff -r 000000000000 -r c51c08cc9fcc test-data/Mutect2-out2.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out2.vcf Wed Dec 29 01:36:41 2021 +0000 |
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| b'@@ -0,0 +1,126 @@\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; will always be heterozygous and is not intended to describe called alleles">\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 tumor.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 --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 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --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 --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-pad'..b'POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1\n+K03455\t7455\t.\tA\tATG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=95;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1\n+K03455\t7457\t.\tTGA\tT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=99;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1\n+K03455\t7460\t.\tCA\tC\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,37;MFRL=0,486;MMQ=60,60;MPOS=100;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1\n+K03455\t7468\t.\tCC\tTA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=107;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7478\t.\tC\tT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=117;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7491\t.\tA\tT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=118;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7494\t.\tA\tG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=115;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7508\t.\tGA\tAG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=101;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7541\t.\tC\tCGA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=68;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7542\t.\tAGT\tA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=65;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7548\t.\tC\tA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=61;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7555\t.\tGA\tAT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=54;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7560\t.\tTC\tGT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,38;MFRL=0,586;MMQ=60,50;MPOS=49;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7568\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=41;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7571\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=38;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7581\t.\tC\tA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=28;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7584\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=25;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7603\t.\tA\tAGGG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,37;MFRL=0,586;MMQ=60,50;MPOS=6;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7604\t.\tT\tG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,33;MFRL=0,586;MMQ=60,50;MPOS=2;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,1:0|1:7541_C_CGA:7541:0,0,0,2\n' |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/Mutect2-out3.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out3.vcf Wed Dec 29 01:36:41 2021 +0000 |
| b |
| b'@@ -0,0 +1,67 @@\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; will always be heterozygous and is not intended to describe called alleles">\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 --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 tumor.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 --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 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --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 -'..b'0,32;MFRL=245,276;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=3.17\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:581,8:0.012:589:285,2:265,5:314,267,4,4\n+K03455\t2872\t.\tT\tA\t.\t.\tAS_SB_TABLE=267,300|25,0;BQHIST=14,1,2,15,2,0,16,0,11,17,6,6,18,15,51,19,0,38,20,0,167,27,1,1,29,0,16,30,0,3,31,0,9,32,0,22,33,0,29,34,0,12,35,0,12,36,0,9,37,0,78,38,0,48,39,0,53;DP=628;ECNT=12;MBQ=29,18;MFRL=240,283;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.43\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:567,25:0.023:592:225,1:234,0:267,300,25,0\n+K03455\t2874\t.\tC\tT\t.\t.\tAS_SB_TABLE=1,0|300,303;BQHIST=16,0,6,17,1,5,18,0,54,19,0,13,20,0,199,29,0,4,30,0,2,31,0,11,32,0,32,33,0,41,34,0,13,35,0,13,36,0,11,37,0,87,38,0,54,39,0,51;DP=606;ECNT=12;MBQ=17,32;MFRL=360,241;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=2043.53\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:1,603:0.997:604:0,265:0,253:1,0,300,303\n+K03455\t2882\t.\tG\tT\t.\t.\tAS_SB_TABLE=1,0|295,283;BQHIST=14,2,0,16,6,0,17,6,0,18,21,0,19,12,0,20,195,0,29,2,0,30,4,0,31,4,1,32,3,0,33,25,0,34,1,0,35,21,0,36,11,0,37,85,0,38,52,0,39,112,0;DP=579;ECNT=12;MBQ=31,35;MFRL=360,246;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1927.63\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:1,578:0.997:579:1,259:0,256:1,0,295,283\n+K03455\t2889\t.\tG\tA\t.\t.\tAS_SB_TABLE=289,272|7,1;BQHIST=14,0,11,15,0,1,16,0,4,17,0,5,18,0,13,19,0,17,20,0,190,29,1,1,30,0,3,31,0,1,32,0,7,33,2,31,34,1,4,35,0,9,36,0,15,37,1,79,38,1,72,39,2,95,40,0,1;DP=580;ECNT=12;MBQ=33,36;MFRL=249,291;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=9.57\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:561,8:0.018:569:248,4:260,4:289,272,7,1\n+K03455\t2891\t.\tA\tG\t.\t.\tAS_SB_TABLE=286,269|5,4;BQHIST=14,0,1,16,6,0,17,9,0,18,18,0,19,8,0,20,179,6,30,1,0,31,4,0,32,8,0,33,25,1,34,2,0,35,26,0,36,7,1,37,78,0,38,85,0,39,89,0;DP=576;ECNT=12;MBQ=35,20;MFRL=249,231;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=8.78\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:555,9:0.013:564:243,4:261,4:286,269,5,4\n+K03455\t2894\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|291,273;BQHIST=14,1,0,15,5,0,16,4,0,17,13,0,18,33,0,19,4,0,20,162,0,27,1,0,29,3,0,30,5,0,31,1,0,32,6,0,33,25,0,34,12,0,35,5,0,36,8,0,37,83,0,38,69,0,39,116,0;DP=564;ECNT=12;MBQ=0,35;MFRL=0,250;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1813.95\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,564:0.998:564:0,243:0,253:0,0,291,273\n+K03455\t2906\t.\tC\tT\t.\t.\tAS_SB_TABLE=0,0|246,262;BQHIST=16,0,2,18,0,4,19,0,10,20,0,145,30,0,2,31,0,2,32,0,3,33,0,21,34,0,3,35,0,19,36,0,11,37,0,61,38,0,79,39,0,146;DP=508;ECNT=12;MBQ=0,37;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2411.23\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,508:0.998:508:0,232:0,260:0|1:2906_C_T:2906:0,0,246,262\n+K03455\t2913\t.\tG\tA\t.\t.\tAS_SB_TABLE=0,0|245,260;BQHIST=18,5,0,19,5,0,20,134,0,29,1,0,30,2,0,31,2,0,32,2,0,33,17,0,34,1,0,35,6,0,36,2,0,37,64,0,38,68,0,39,184,0,40,4,0;DP=505;ECNT=12;MBQ=0,38;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2402.33\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,505:0.998:505:0,230:0,257:0|1:2906_C_T:2906:0,0,245,260\n+K03455\t2987\t.\tC\tT\t.\t.\tAS_SB_TABLE=0,0|86,133;BQHIST=16,0,3,17,0,3,19,0,11,20,0,15,30,0,2,31,0,9,32,0,7,33,0,31,34,0,8,35,0,9,36,0,1,37,0,47,38,0,34,39,0,39;DP=223;ECNT=4;MBQ=0,37;MFRL=0,264;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=847.13\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.\tAS_SB_TABLE=74,105|9,0;BQHIST=16,1,0,17,3,0,18,1,7,19,23,0,20,13,1,29,1,0,31,8,0,32,8,0,33,18,1,34,9,0,35,4,0,36,4,0,37,35,0,38,30,0,39,21,0;DP=206;ECNT=4;MBQ=36,18;MFRL=271,260;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.85\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.\tAS_SB_TABLE=61,27|7,0;BQHIST=14,0,2,15,0,2,18,6,26,29,0,1,30,0,3,32,0,5,33,1,12,34,0,2,35,0,2,36,0,8,37,0,5,38,0,16,39,0,4;DP=100;ECNT=4;MBQ=33,18;MFRL=276,255;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=5.62\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.\tAS_SB_TABLE=0,0|65,25;BQHIST=14,0,12,16,0,1,18,0,1,27,0,3,29,0,3,30,0,8,32,0,8,33,0,2,34,0,1,35,0,1,36,0,21,37,0,4,38,0,23,39,0,1;DP=95;ECNT=4;MBQ=0,36;MFRL=0,284;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=324.41\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 c51c08cc9fcc test-data/Mutect2-out4.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out4.vcf Wed Dec 29 01:36:41 2021 +0000 |
| 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; will always be heterozygous and is not intended to describe called alleles">\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 tumor.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 --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 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --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 --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padd'..b'POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1\n+K03455\t7455\t.\tA\tATG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=95;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1\n+K03455\t7457\t.\tTGA\tT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=99;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1\n+K03455\t7460\t.\tCA\tC\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=1;ECNT=23;MBQ=0,37;MFRL=0,486;MMQ=60,60;MPOS=100;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1\n+K03455\t7468\t.\tCC\tTA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=107;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7478\t.\tC\tT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=117;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7491\t.\tA\tT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=118;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7494\t.\tA\tG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=115;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7508\t.\tGA\tAG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=101;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2\n+K03455\t7541\t.\tC\tCGA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=68;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7542\t.\tAGT\tA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=65;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7548\t.\tC\tA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=61;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7555\t.\tGA\tAT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=54;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7560\t.\tTC\tGT\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,38;MFRL=0,586;MMQ=60,50;MPOS=49;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7568\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=41;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7571\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=38;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7581\t.\tC\tA\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=28;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7584\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=25;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7603\t.\tA\tAGGG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,37;MFRL=0,586;MMQ=60,50;MPOS=6;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2\n+K03455\t7604\t.\tT\tG\t.\t.\tAS_SB_TABLE=0,0|0,0;DP=2;ECNT=23;MBQ=0,33;MFRL=0,586;MMQ=60,50;MPOS=2;POPAF=7.30;TLOD=8.70\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:0,2:0.667:2:0,0:0,1:0|1:7541_C_CGA:7541:0,0,0,2\n' |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/Mutect2-out5-1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out5-1.tabular Wed Dec 29 01:36:41 2021 +0000 |
| 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 c51c08cc9fcc test-data/Mutect2-out5-2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out5-2.tabular Wed Dec 29 01:36:41 2021 +0000 |
| 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 c51c08cc9fcc test-data/Mutect2-out5.bam |
| b |
| Binary file test-data/Mutect2-out5.bam has changed |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/Mutect2-out5.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out5.vcf Wed Dec 29 01:36:41 2021 +0000 |
| b |
| b'@@ -0,0 +1,94 @@\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; will always be heterozygous and is not intended to describe called alleles">\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 --assembly-region-out assembly-region.tab --input tumor.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 --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 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --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 --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads'..b'PAF=7.30;TLOD=12.44\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:39,5:0.098:44:23,2:16,3:0|1:2200_ACTC_A:2200:27,12,3,2\n+K03455\t2258\t.\tGG\tAA\t.\t.\tAS_SB_TABLE=6,0|26,14;DP=46;ECNT=41;MBQ=39,39;MFRL=216,239;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=159.02\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:6,40:0.859:46:3,22:3,17:0|1:2258_GG_AA:2258:6,0,26,14\n+K03455\t2259\t.\tG\tA\t.\t.\tAS_SB_TABLE=0,0|10,3;DP=46;ECNT=41;MBQ=0,37;MFRL=0,241;MMQ=60,60;MPOS=39;POPAF=7.30;TLOD=13.48\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t1|0:0,13:0.961:13:0,5:0,8:1|0:2258_GG_AA:2258:0,0,10,3\n+K03455\t2282\t.\tC\tT\t.\t.\tAS_SB_TABLE=32,24|2,2;DP=60;ECNT=41;MBQ=36,20;MFRL=239,182;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=9.01\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:56,4:0.059:60:24,1:24,2:32,24,2,2\n+K03455\t2285\t.\tC\tT\t.\t.\tAS_SB_TABLE=30,23|6,3;DP=62;ECNT=41;MBQ=29,38;MFRL=236,205;MMQ=60,60;MPOS=49;POPAF=7.30;TLOD=26.48\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:53,9:0.151:62:24,3:21,4:30,23,6,3\n+K03455\t2287\t.\tCA\tAT\t.\t.\tAS_SB_TABLE=32,26|4,3;DP=65;ECNT=41;MBQ=33,37;MFRL=234,285;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=17.41\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:58,7:0.133:65:25,1:24,2:32,26,4,3\n+K03455\t2300\t.\tG\tA\t.\t.\tAS_SB_TABLE=6,6|26,23;DP=63;ECNT=41;MBQ=31,32;MFRL=229,236;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=211.84\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:12,49:0.796:61:3,20:5,22:6,6,26,23\n+K03455\t2303\t.\tGCA\tG\t.\t.\tAS_SB_TABLE=7,8|25,20;DP=61;ECNT=41;MBQ=36,31;MFRL=225,241;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=171.69\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:15,45:0.735:60:2,18:9,20:7,8,25,20\n+K03455\t2304\t.\tCAA\tGTG\t.\t.\tAS_SB_TABLE=6,6|10,9;DP=61;ECNT=41;MBQ=33,20;MFRL=229,235;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=3.47\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:12,19:0.531:31:4,0:7,3:6,6,10,9\n+K03455\t2306\t.\tA\tATG,G\t.\t.\tAS_SB_TABLE=2,2|26,22|4,4;DP=60;ECNT=41;MBQ=29,32,33;MFRL=182,239,280;MMQ=60,60,60;MPOS=39,19;POPAF=7.30,7.30;TLOD=175.97,22.08\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1/2:4,48,8:0.779,0.164:60:2,20,2:2,23,4:2,2,30,26\n+K03455\t2315\t.\tA\tG\t.\t.\tAS_SB_TABLE=19,19|11,9;DP=59;ECNT=41;MBQ=37,38;MFRL=229,244;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=74.64\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:38,20:0.379:58:17,6:15,14:0|1:2315_A_G:2315:19,19,11,9\n+K03455\t2321\t.\tA\tC\t.\t.\tAS_SB_TABLE=17,19|11,9;DP=56;ECNT=41;MBQ=34,37;MFRL=229,244;MMQ=60,60;MPOS=49;POPAF=7.30;TLOD=75.24\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:36,20:0.392:56:16,6:17,14:0|1:2315_A_G:2315:17,19,11,9\n+K03455\t2349\t.\tT\tC\t.\t.\tAS_SB_TABLE=23,24|4,5;DP=56;ECNT=9;MBQ=35,35;MFRL=235,285;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=28.30\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:47,9:0.190:56:19,3:22,5:23,24,4,5\n+K03455\t2360\t.\tG\tA\t.\t.\tAS_SB_TABLE=19,20|4,6;DP=49;ECNT=9;MBQ=37,27;MFRL=235,272;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=28.07\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:39,10:0.229:49:15,3:22,3:19,20,4,6\n+K03455\t2362\t.\tG\tA\t.\t.\tAS_SB_TABLE=0,0|21,26;DP=49;ECNT=9;MBQ=0,36;MFRL=0,241;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=181.58\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,47:0.978:47:0,19:0,25:0,0,21,26\n+K03455\t2372\t.\tA\tG\t.\t.\tAS_SB_TABLE=16,19|4,5;DP=44;ECNT=9;MBQ=37,36;MFRL=241,259;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=30.36\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:35,9:0.234:44:9,3:17,5:16,19,4,5\n+K03455\t2374\t.\tG\tA\t.\t.\tAS_SB_TABLE=12,22|2,2;DP=38;ECNT=9;MBQ=37,35;MFRL=234,284;MMQ=60,60;MPOS=7;POPAF=7.30;TLOD=7.75\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:34,4:0.118:38:8,1:20,2:12,22,2,2\n+K03455\t2423\t.\tA\tG\t.\t.\tAS_SB_TABLE=0,13|0,3;DP=16;ECNT=9;MBQ=34,33;MFRL=255,199;MMQ=60,60;MPOS=16;POPAF=7.30;TLOD=8.83\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:13,3:0.226:16:3,0:9,3:0,13,0,3\n+K03455\t2436\t.\tA\tG\t.\t.\tAS_SB_TABLE=0,1|0,4;DP=6;ECNT=9;MBQ=16,31;MFRL=255,240;MMQ=60,60;MPOS=4;POPAF=7.30;TLOD=16.53\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:1,4:0.725:5:0,0:0,4:0,1,0,4\n+K03455\t2438\t.\tA\tG\t.\t.\tAS_SB_TABLE=0,3|0,2;DP=6;ECNT=9;MBQ=29,33;MFRL=255,255;MMQ=60,60;MPOS=3;POPAF=7.30;TLOD=7.20\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:3,2:0.430:5:0,0:2,2:0|1:2438_A_G:2438:0,3,0,2\n+K03455\t2440\t.\tT\tC\t.\t.\tAS_SB_TABLE=0,3|0,2;DP=6;ECNT=9;MBQ=0,31;MFRL=255,255;MMQ=60,60;MPOS=1;POPAF=7.30;TLOD=7.20\tGT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB\t0|1:3,2:0.430:5:0,0:0,2:0|1:2438_A_G:2438:0,3,0,2\n' |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/Mutect2-out6.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out6.vcf Wed Dec 29 01:36:41 2021 +0000 |
| b |
| b'@@ -0,0 +1,64 @@\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; will always be heterozygous and is not intended to describe called alleles">\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 NA12891 --output output.vcf --input tumor.bam --input normal.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 --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 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --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 --allele-informative-reads-overlap-margin 2 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-reads-per-alignment-start 50 --interval-set-rule UNION'..b'.\tC\tCTAT\t.\t.\tAS_SB_TABLE=19,18|4,5;DP=50;ECNT=1;MBQ=38,39;MFRL=351,362;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=1,2;RU=TAT;STR;TLOD=29.75\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:11,9:0.454:20:4,4:6,4:5,6,4,5\t0/1:26,0:0.034:26:14,0:11,0:14,12,0,0\n+chr20\t863271\t.\tA\tG\t.\t.\tAS_SB_TABLE=24,10|5,4;DP=44;ECNT=1;MBQ=36,37;MFRL=347,359;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=26.85\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:8,9:0.526:17:4,5:4,4:7,1,5,4\t0/1:26,0:0.035:26:15,0:10,0:17,9,0,0\n+chr20\t863508\t.\tA\tG\t.\t.\tAS_SB_TABLE=24,20|6,6;DP=59;ECNT=1;MBQ=39,40;MFRL=343,355;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=36.80\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:11,12:0.524:23:6,6:4,6:4,7,6,6\t0/1:33,0:0.028:33:16,0:16,0:20,13,0,0\n+chr20\t863706\t.\tC\tT\t.\t.\tAS_SB_TABLE=7,25|9,11;DP=53;ECNT=2;MBQ=37,39;MFRL=341,345;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=65.75\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,20:0.955:20:0,12:0,7:0,0,9,11\t0/1:32,0:0.029:32:9,0:23,0:7,25,0,0\n+chr20\t863744\t.\tC\tT\t.\t.\tAS_SB_TABLE=10,24|6,6;DP=48;ECNT=2;MBQ=39,38;MFRL=341,347;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=38.56\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:8,12:0.591:20:5,7:3,5:4,4,6,6\t0/1:26,0:0.035:26:10,0:16,0:6,20,0,0\n+chr20\t863846\t.\tC\tT\t.\t.\tAS_SB_TABLE=28,10|4,3;DP=48;ECNT=2;MBQ=40,38;MFRL=348,343;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=20.26\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:17,7:0.309:24:11,5:5,2:14,3,4,3\t0/1:21,0:0.042:21:9,0:12,0:14,7,0,0\n+chr20\t863873\t.\tC\tT\t.\t.\tAS_SB_TABLE=23,11|7,3;DP=48;ECNT=2;MBQ=39,37;MFRL=353,337;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=30.15\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:21,0:0.041:21:14,0:6,0:15,6,0,0\t0/1:13,10:0.440:23:8,3:5,7:8,5,7,3\n+chr20\t864074\t.\tT\tC\t.\t.\tAS_SB_TABLE=19,20|8,3;DP=53;ECNT=1;MBQ=38,36;MFRL=344,355;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=31.98\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:13,11:0.465:24:7,9:5,2:5,8,8,3\t0/1:26,0:0.035:26:13,0:13,0:14,12,0,0\n+chr20\t864199\t.\tG\tA\t.\t.\tAS_SB_TABLE=30,18|4,9;DP=63;ECNT=1;MBQ=36,39;MFRL=343,361;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=37.97\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:15,13:0.470:28:7,7:7,6:13,2,4,9\t0/1:33,0:0.028:33:23,0:10,0:17,16,0,0\n+chr20\t864301\t.\tG\tT\t.\t.\tAS_SB_TABLE=20,17|12,6;DP=57;ECNT=1;MBQ=35,35;MFRL=344,358;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=56.37\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:12,18:0.594:30:9,12:3,6:6,6,12,6\t0/1:25,0:0.036:25:11,0:14,0:14,11,0,0\n+chr20\t864455\t.\tT\tC\t.\t.\tAS_SB_TABLE=11,17|15,17;DP=63;ECNT=2;MBQ=35,39;MFRL=343,360;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=115.14\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,32:0.971:32:0,16:0,16:0,0,15,17\t0/1:28,0:0.033:28:19,0:8,0:11,17,0,0\n+chr20\t864512\t.\tA\tG\t.\t.\tAS_SB_TABLE=17,22|11,15;DP=71;ECNT=2;MBQ=38,37;MFRL=344,364;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=88.07\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:14,26:0.647:40:8,12:5,14:9,5,11,15\t0/1:25,0:0.035:25:12,0:12,0:8,17,0,0\n+chr20\t864640\t.\tC\tT\t.\t.\tAS_SB_TABLE=16,18|14,14;DP=64;ECNT=2;MBQ=38,35;MFRL=339,354;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=94.78\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,28:0.968:28:0,11:0,17:0,0,14,14\t0/1:34,0:0.028:34:22,0:12,0:16,18,0,0\n+chr20\t864660\t.\tG\tT\t.\t.\tAS_SB_TABLE=16,15|11,11;DP=55;ECNT=2;MBQ=37,38;MFRL=340,358;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=69.72\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,22:0.960:22:0,8:0,12:0,0,11,11\t0/1:31,0:0.030:31:17,0:13,0:16,15,0,0\n+chr20\t865054\t.\tG\tC\t.\t.\tAS_SB_TABLE=10,8|6,4;DP=30;ECNT=1;MBQ=35,34;MFRL=347,347;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=30.15\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:9,10:0.524:19:7,6:2,4:6,3,6,4\t0/1:9,0:0.092:9:3,0:5,0:4,5,0,0\n+chr20\t865366\t.\tG\tT\t.\t.\tAS_SB_TABLE=13,13|15,11;DP=54;ECNT=1;MBQ=39,37;MFRL=343,353;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=88.44\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,26:0.965:26:0,14:0,10:0,0,15,11\t0/1:26,0:0.035:26:10,0:16,0:13,13,0,0\n+chr20\t865537\t.\tC\tT\t.\t.\tAS_SB_TABLE=17,29|6,3;DP=58;ECNT=1;MBQ=35,35;MFRL=350,358;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=24.37\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:19,9:0.333:28:10,4:9,5:8,11,6,3\t0/1:27,0:0.034:27:13,0:13,0:9,18,0,0\n+chr20\t865664\t.\tTC\tT\t.\t.\tAS_SB_TABLE=20,20|7,10;DP=59;ECNT=1;MBQ=35,34;MFRL=348,359;MMQ=60,60;MPOS=25;POPAF=7.30;RPA=4,3;RU=C;STR;TLOD=42.63\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:19,17:0.474:36:10,11:9,4:11,8,7,10\t0/1:21,0:0.043:21:7,0:10,0:9,12,0,0\n' |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/Mutect2-out6.vcf_bgzip |
| b |
| Binary file test-data/Mutect2-out6.vcf_bgzip has changed |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/Mutect2-out6.vcf_bgzip.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out6.vcf_bgzip.stats Wed Dec 29 01:36:41 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +statistic value +callable 3152.0 |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Wed Dec 29 01:36:41 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +hg38 hg38 Human hg38 ${__HERE__}/cached_locally/cached_reference.fa |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/cached_locally/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/all_fasta.loc Wed Dec 29 01:36:41 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +hg38 hg38 Human hg38 ${__HERE__}/cached_reference.fa |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/cached_locally/cached_reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/cached_reference.fa Wed Dec 29 01:36:41 2021 +0000 |
| b |
| b'@@ -0,0 +1,2 @@\n+>K03455\n+TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCA'..b'CAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA\n' |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/chr20.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr20.fa Wed Dec 29 01:36:41 2021 +0000 |
| b |
| b'@@ -0,0 +1,1050427 @@\n+>chr20\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+'..b'NNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN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|
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/filtered_Mutect2-out1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered_Mutect2-out1.vcf Wed Dec 29 01:36:41 2021 +0000 |
| b |
| b'@@ -0,0 +1,118 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">\n+##FILTER=<ID=PASS,Description="Site contains at least one allele that passes filters">\n+##FILTER=<ID=base_qual,Description="alt median base quality">\n+##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">\n+##FILTER=<ID=contamination,Description="contamination">\n+##FILTER=<ID=duplicate,Description="evidence for alt allele is overrepresented by apparent duplicates">\n+##FILTER=<ID=fragment,Description="abs(ref - alt) median fragment length">\n+##FILTER=<ID=germline,Description="Evidence indicates this site is germline, not somatic">\n+##FILTER=<ID=haplotype,Description="Variant near filtered variant on same haplotype.">\n+##FILTER=<ID=low_allele_frac,Description="Allele fraction is below specified threshold">\n+##FILTER=<ID=map_qual,Description="ref - alt median mapping quality">\n+##FILTER=<ID=multiallelic,Description="Site filtered because too many alt alleles pass tumor LOD">\n+##FILTER=<ID=n_ratio,Description="Ratio of N to alt exceeds specified ratio">\n+##FILTER=<ID=normal_artifact,Description="artifact_in_normal">\n+##FILTER=<ID=orientation,Description="orientation bias detected by the orientation bias mixture model">\n+##FILTER=<ID=panel_of_normals,Description="Blacklisted site in panel of normals">\n+##FILTER=<ID=position,Description="median distance of alt variants from end of reads">\n+##FILTER=<ID=possible_numt,Description="Allele depth is below expected coverage of NuMT in autosome">\n+##FILTER=<ID=slippage,Description="Site filtered due to contraction of short tandem repeat region">\n+##FILTER=<ID=strand_bias,Description="Evidence for alt allele comes from one read direction only">\n+##FILTER=<ID=strict_strand,Description="Evidence for alt allele is not represented in both directions">\n+##FILTER=<ID=weak_evidence,Description="Mutation does not meet likelihood threshold">\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; will always be heterozygous and is not intended to describe called alleles">\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=FilterMutectCalls,CommandLine="FilterMutectCalls --output filtered.vcf --variant input.vcf --reference reference.fa --QUIET true --threshold-strategy OPTIMAL_F_SCORE --f-score-beta 1.0 --false-discovery-rate 0.05 --initial-threshold 0.1 --mitochondria-mode false --max-events-in-region 2 --max-alt-allele-count 1 --unique-alt-read-count 0 --min-median-mapping-quality 30 --min-median-base-quality 20 --max-median-fragment-length-differenc'..b'AS_SB_TABLE=25,37|1,2;DP=65;ECNT=21;GERMQ=93;MBQ=37,36;MFRL=280,300;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=7.02\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:62,3:0.063:65:26,2:32,1:25,37,1,2\n+K03455\t4439\t.\tA\tG\t.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=22,31|3,4;DP=60;ECNT=21;GERMQ=59;MBQ=38,35;MFRL=287,210;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=21.26\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:53,7:0.121:60:23,3:26,4:22,31,3,4\n+K03455\t4442\t.\tAG\tGA\t.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=21,30|3,4;DP=59;ECNT=21;GERMQ=54;MBQ=37,33;MFRL=287,209;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=18.12\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:51,7:0.142:58:20,2:25,5:21,30,3,4\n+K03455\t4443\t.\tG\tA\t.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=12,19|11,12;DP=59;ECNT=21;GERMQ=1;MBQ=35,38;MFRL=276,291;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=78.51\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:31,23:0.421:54:14,10:13,10:12,19,11,12\n+K03455\t4448\t.\tC\tA\t.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=22,31|1,2;DP=57;ECNT=21;GERMQ=89;MBQ=37,20;MFRL=287,126;MMQ=60,60;MPOS=25;POPAF=7.30;TLOD=8.91\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:53,3:0.055:56:21,0:27,2:22,31,1,2\n+K03455\t4449\t.\tC\tT\t.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=13,16|11,15;DP=55;ECNT=21;GERMQ=1;MBQ=37,38;MFRL=209,322;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=97.76\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:29,26:0.491:55:11,12:16,13:13,16,11,15\n+K03455\t4460\t.\tT\tC\t.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=22,22|2,5;DP=51;ECNT=21;GERMQ=38;MBQ=37,37;MFRL=279,321;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=22.02\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:44,7:0.163:51:17,3:24,3:22,22,2,5\n+K03455\t4465\t.\tT\tTGGCC\t.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=19,20|4,4;DP=50;ECNT=21;GERMQ=17;MBQ=37,35;MFRL=290,176;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=26.66\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:39,8:0.155:47:14,6:22,1:19,20,4,4\n+K03455\t4466\t.\tA\tG,AGTG\t.\tclustered_events;multiallelic\tAS_FilterStatus=SITE|SITE;AS_SB_TABLE=16,17|2,3|4,4;DP=49;ECNT=21;GERMQ=15;MBQ=37,38,37;MFRL=310,207,176;MMQ=60,60,60;MPOS=20,25;POPAF=7.30,7.30;TLOD=15.50,28.09\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1/2:33,5,8:0.154,0.179:46:12,1,6:16,4,1:16,17,6,7\n+K03455\t4478\t.\tT\tC\t.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=12,13|5,6;DP=36;ECNT=21;GERMQ=1;MBQ=37,32;MFRL=323,205;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=44.55\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:25,11:0.306:36:9,6:15,4:12,13,5,6\n+K03455\t4505\t.\tA\tG\t.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=2,1|11,6;DP=20;ECNT=21;GERMQ=5;MBQ=39,37;MFRL=394,323;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=72.12\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:3,17:0.818:20:2,6:1,8:2,1,11,6\n+K03455\t4508\t.\tA\tT\t.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=2,3|10,3;DP=18;ECNT=21;GERMQ=1;MBQ=39,35;MFRL=287,335;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=52.71\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:5,13:0.700:18:3,5:2,8:2,3,10,3\n+K03455\t4511\t.\tG\tA\t.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=2,1|10,5;DP=18;ECNT=21;GERMQ=3;MBQ=37,35;MFRL=394,323;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=62.74\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:3,15:0.800:18:2,5:1,7:2,1,10,5\n+K03455\t4526\t.\tT\tC\t.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=0,0|11,2;DP=13;ECNT=21;GERMQ=18;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.\tclustered_events;haplotype\tAS_FilterStatus=SITE;AS_SB_TABLE=10,1|1,1;DP=13;ECNT=21;GERMQ=1;MBQ=38,37;MFRL=323,421;MMQ=60,60;MPOS=38;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.\tclustered_events;haplotype\tAS_FilterStatus=SITE;AS_SB_TABLE=9,1|1,1;DP=13;ECNT=21;GERMQ=1;MBQ=35,38;MFRL=323,421;MMQ=60,60;MPOS=34;POPAF=7.30;RPA=4,2;RU=T;STR;STRQ=93;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.\tclustered_events\tAS_FilterStatus=SITE;AS_SB_TABLE=0,0|11,0;DP=13;ECNT=21;GERMQ=13;MBQ=0,27;MFRL=0,323;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=39.42\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,11:0.926:11:0,6:0,2:0,0,11,0\n' |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/filtered_Mutect2-out1_stats.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered_Mutect2-out1_stats.tsv Wed Dec 29 01:36:41 2021 +0000 |
| b |
| @@ -0,0 +1,27 @@ +#<METADATA>Ln prior of deletion of length 10=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 9=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 8=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 7=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 6=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 5=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 4=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 3=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 2=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 1=-20.72326583694641 +#<METADATA>Ln prior of SNV=-18.420680743952367 +#<METADATA>Ln prior of insertion of length 1=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 2=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 3=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 4=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 5=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 6=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 7=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 8=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 9=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 10=-20.72326583694641 +#<METADATA>Background beta-binomial cluster=weight = 0.5000, alpha = 1.00, beta = 1.00 +#<METADATA>High-AF beta-binomial cluster=weight = 0.5000, alpha = 10.00, beta = 1.00 +#<METADATA>threshold=1.0 +#<METADATA>fdr=0.0 +#<METADATA>sensitivity=0.0 +filter FP FDR FN FNR |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/filtered_Mutect2-out6.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered_Mutect2-out6.vcf Wed Dec 29 01:36:41 2021 +0000 |
| b |
| b'@@ -0,0 +1,89 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">\n+##FILTER=<ID=PASS,Description="Site contains at least one allele that passes filters">\n+##FILTER=<ID=base_qual,Description="alt median base quality">\n+##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">\n+##FILTER=<ID=contamination,Description="contamination">\n+##FILTER=<ID=duplicate,Description="evidence for alt allele is overrepresented by apparent duplicates">\n+##FILTER=<ID=fragment,Description="abs(ref - alt) median fragment length">\n+##FILTER=<ID=germline,Description="Evidence indicates this site is germline, not somatic">\n+##FILTER=<ID=haplotype,Description="Variant near filtered variant on same haplotype.">\n+##FILTER=<ID=low_allele_frac,Description="Allele fraction is below specified threshold">\n+##FILTER=<ID=map_qual,Description="ref - alt median mapping quality">\n+##FILTER=<ID=multiallelic,Description="Site filtered because too many alt alleles pass tumor LOD">\n+##FILTER=<ID=n_ratio,Description="Ratio of N to alt exceeds specified ratio">\n+##FILTER=<ID=normal_artifact,Description="artifact_in_normal">\n+##FILTER=<ID=orientation,Description="orientation bias detected by the orientation bias mixture model">\n+##FILTER=<ID=panel_of_normals,Description="Blacklisted site in panel of normals">\n+##FILTER=<ID=position,Description="median distance of alt variants from end of reads">\n+##FILTER=<ID=possible_numt,Description="Allele depth is below expected coverage of NuMT in autosome">\n+##FILTER=<ID=slippage,Description="Site filtered due to contraction of short tandem repeat region">\n+##FILTER=<ID=strand_bias,Description="Evidence for alt allele comes from one read direction only">\n+##FILTER=<ID=strict_strand,Description="Evidence for alt allele is not represented in both directions">\n+##FILTER=<ID=weak_evidence,Description="Mutation does not meet likelihood threshold">\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; will always be heterozygous and is not intended to describe called alleles">\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=FilterMutectCalls,CommandLine="FilterMutectCalls --output filtered.vcf --variant input.vcf --reference reference.fa --QUIET true --threshold-strategy OPTIMAL_F_SCORE --f-score-beta 1.0 --false-discovery-rate 0.05 --initial-threshold 0.1 --mitochondria-mode false --max-events-in-region 2 --max-alt-allele-count 1 --unique-alt-read-count 0 --min-median-mapping-quality 30 --min-median-base-quality 20 --max-median-fragment-length-difference'..b'MBQ=39,40;MFRL=343,355;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=36.80\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:11,12:0.524:23:6,6:4,6:4,7,6,6\t0/1:33,0:0.028:33:16,0:16,0:20,13,0,0\n+chr20\t863706\t.\tC\tT\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=7,25|9,11;DP=53;ECNT=2;GERMQ=40;MBQ=37,39;MFRL=341,345;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=65.75\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,20:0.955:20:0,12:0,7:0,0,9,11\t0/1:32,0:0.029:32:9,0:23,0:7,25,0,0\n+chr20\t863744\t.\tC\tT\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=10,24|6,6;DP=48;ECNT=2;GERMQ=64;MBQ=39,38;MFRL=341,347;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=38.56\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:8,12:0.591:20:5,7:3,5:4,4,6,6\t0/1:26,0:0.035:26:10,0:16,0:6,20,0,0\n+chr20\t863846\t.\tC\tT\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=28,10|4,3;DP=48;ECNT=2;GERMQ=88;MBQ=40,38;MFRL=348,343;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=20.26\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:17,7:0.309:24:11,5:5,2:14,3,4,3\t0/1:21,0:0.042:21:9,0:12,0:14,7,0,0\n+chr20\t863873\t.\tC\tT\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=23,11|7,3;DP=48;ECNT=2;GERMQ=70;MBQ=39,37;MFRL=353,337;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=30.15\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:21,0:0.041:21:14,0:6,0:15,6,0,0\t0/1:13,10:0.440:23:8,3:5,7:8,5,7,3\n+chr20\t864074\t.\tT\tC\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=19,20|8,3;DP=53;ECNT=1;GERMQ=76;MBQ=38,36;MFRL=344,355;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=31.98\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:13,11:0.465:24:7,9:5,2:5,8,8,3\t0/1:26,0:0.035:26:13,0:13,0:14,12,0,0\n+chr20\t864199\t.\tG\tA\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=30,18|4,9;DP=63;ECNT=1;GERMQ=86;MBQ=36,39;MFRL=343,361;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=37.97\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:15,13:0.470:28:7,7:7,6:13,2,4,9\t0/1:33,0:0.028:33:23,0:10,0:17,16,0,0\n+chr20\t864301\t.\tG\tT\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=20,17|12,6;DP=57;ECNT=1;GERMQ=52;MBQ=35,35;MFRL=344,358;MMQ=60,60;MPOS=28;POPAF=7.30;TLOD=56.37\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:12,18:0.594:30:9,12:3,6:6,6,12,6\t0/1:25,0:0.036:25:11,0:14,0:14,11,0,0\n+chr20\t864455\t.\tT\tC\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=11,17|15,17;DP=63;ECNT=2;GERMQ=33;MBQ=35,39;MFRL=343,360;MMQ=60,60;MPOS=27;POPAF=7.30;TLOD=115.14\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,32:0.971:32:0,16:0,16:0,0,15,17\t0/1:28,0:0.033:28:19,0:8,0:11,17,0,0\n+chr20\t864512\t.\tA\tG\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=17,22|11,15;DP=71;ECNT=2;GERMQ=39;MBQ=38,37;MFRL=344,364;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=88.07\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:14,26:0.647:40:8,12:5,14:9,5,11,15\t0/1:25,0:0.035:25:12,0:12,0:8,17,0,0\n+chr20\t864640\t.\tC\tT\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=16,18|14,14;DP=64;ECNT=2;GERMQ=34;MBQ=38,35;MFRL=339,354;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=94.78\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,28:0.968:28:0,11:0,17:0,0,14,14\t0/1:34,0:0.028:34:22,0:12,0:16,18,0,0\n+chr20\t864660\t.\tG\tT\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=16,15|11,11;DP=55;ECNT=2;GERMQ=37;MBQ=37,38;MFRL=340,358;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=69.72\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,22:0.960:22:0,8:0,12:0,0,11,11\t0/1:31,0:0.030:31:17,0:13,0:16,15,0,0\n+chr20\t865054\t.\tG\tC\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=10,8|6,4;DP=30;ECNT=1;GERMQ=43;MBQ=35,34;MFRL=347,347;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=30.15\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:9,10:0.524:19:7,6:2,4:6,3,6,4\t0/1:9,0:0.092:9:3,0:5,0:4,5,0,0\n+chr20\t865366\t.\tG\tT\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=13,13|15,11;DP=54;ECNT=1;GERMQ=33;MBQ=39,37;MFRL=343,353;MMQ=60,60;MPOS=24;POPAF=7.30;TLOD=88.44\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:0,26:0.965:26:0,14:0,10:0,0,15,11\t0/1:26,0:0.035:26:10,0:16,0:13,13,0,0\n+chr20\t865537\t.\tC\tT\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=17,29|6,3;DP=58;ECNT=1;GERMQ=93;MBQ=35,35;MFRL=350,358;MMQ=60,60;MPOS=21;POPAF=7.30;TLOD=24.37\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:19,9:0.333:28:10,4:9,5:8,11,6,3\t0/1:27,0:0.034:27:13,0:13,0:9,18,0,0\n+chr20\t865664\t.\tTC\tT\t.\tPASS\tAS_FilterStatus=SITE;AS_SB_TABLE=20,20|7,10;DP=59;ECNT=1;GERMQ=52;MBQ=35,34;MFRL=348,359;MMQ=60,60;MPOS=25;POPAF=7.30;RPA=4,3;RU=C;STR;STRQ=93;TLOD=42.63\tGT:AD:AF:DP:F1R2:F2R1:SB\t0/1:19,17:0.474:36:10,11:9,4:11,8,7,10\t0/1:21,0:0.043:21:7,0:10,0:9,12,0,0\n' |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/filtered_Mutect2-out6.vcf_bgzip |
| b |
| Binary file test-data/filtered_Mutect2-out6.vcf_bgzip has changed |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/filtered_Mutect2-out6_stats.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered_Mutect2-out6_stats.tsv Wed Dec 29 01:36:41 2021 +0000 |
| b |
| @@ -0,0 +1,31 @@ +#<METADATA>Ln prior of deletion of length 10=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 9=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 8=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 7=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 6=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 5=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 4=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 3=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 2=-20.72326583694641 +#<METADATA>Ln prior of deletion of length 1=-8.055798885543242 +#<METADATA>Ln prior of SNV=-5.222811848329794 +#<METADATA>Ln prior of insertion of length 1=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 2=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 3=-8.055792507842842 +#<METADATA>Ln prior of insertion of length 4=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 5=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 6=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 7=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 8=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 9=-20.72326583694641 +#<METADATA>Ln prior of insertion of length 10=-20.72326583694641 +#<METADATA>Background beta-binomial cluster=weight = 0.4314, alpha = 1.84, beta = 2.65 +#<METADATA>High-AF beta-binomial cluster=weight = 0.0459, alpha = 9.99, beta = 1.03 +#<METADATA>Binomial cluster=weight = 0.5227, mean = 0.237 +#<METADATA>threshold=1.0 +#<METADATA>fdr=0.0 +#<METADATA>sensitivity=1.0 +filter FP FDR FN FNR +weak_evidence 0.0 0.0 0.0 0.0 +strand_bias 0.0 0.0 0.0 0.0 +germline 0.0 0.0 0.0 0.0 |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/normal.bam |
| b |
| Binary file test-data/normal.bam has changed |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fa Wed Dec 29 01:36:41 2021 +0000 |
| b |
| b'@@ -0,0 +1,2 @@\n+>K03455\n+TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCA'..b'CAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA\n' |
| b |
| diff -r 000000000000 -r c51c08cc9fcc test-data/tumor.bam |
| b |
| Binary file test-data/tumor.bam has changed |
| b |
| diff -r 000000000000 -r c51c08cc9fcc tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Wed Dec 29 01:36:41 2021 +0000 |
| 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 c51c08cc9fcc 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 Dec 29 01:36:41 2021 +0000 |
| 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> |
| b |
| diff -r 000000000000 -r c51c08cc9fcc tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Dec 29 01:36:41 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> |