Mercurial > repos > iuc > gatk4_mutect2
diff test-data/Mutect2-out4.vcf @ 0:f41a1e03538b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
| author | iuc |
|---|---|
| date | Wed, 30 Oct 2019 15:33:59 -0400 |
| parents | |
| children | fd2d6e035c3f |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out4.vcf Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,75 @@ +##fileformat=VCFv4.2 +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> +##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> +##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --max-population-af 0.01 --downsampling-stride 1 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --dont-trim-active-regions true --num-pruning-samples 1 --min-dangling-branch-length 4 --max-num-haplotypes-in-population 128 --min-pruning 2 --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 1 --bam-writer-type CALLED_HAPLOTYPES --min-base-quality-score 10 --smith-waterman FASTEST_AVAILABLE --max-mnp-distance 1 --output output.vcf --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --interval-padding 0 --interval-merging-rule ALL --input input.bam --reference reference.fa --QUIET true --gcs-max-retries 20 --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --pcr-snv-qual 40 --pcr-indel-qual 40 --callable-depth 10 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --recover-all-dangling-branches false --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --native-pair-hmm-use-double-precision false --dont-use-soft-clipped-bases false --emit-ref-confidence NONE --force-call-filtered-alleles false --force-active false --interval-set-rule UNION --interval-exclusion-padding 0 --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --use-jdk-deflater false --use-jdk-inflater false --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="October 29, 2019 1:15:43 PM EDT"> +##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> +##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> +##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> +##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals"> +##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles"> +##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact"> +##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> +##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> +##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors"> +##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> +##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact"> +##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors"> +##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing"> +##INFO=<ID=UNIQ_ALT_READ_COUNT,Number=1,Type=Integer,Description="Number of ALT reads with unique start and mate end positions at a variant site"> +##MutectVersion=2.2 +##contig=<ID=K03455,length=9719> +##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives. +##source=Mutect2 +##tumor_sample=SRR8525881 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 +K03455 6822 . GT AC . . DP=2;ECNT=1;MBQ=0,29;MFRL=0,117;MMQ=60,60;MPOS=79;POPAF=7.30;TLOD=8.52 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,2:0.750:2:0,0:0,2:0,0,0,2 +K03455 6902 . A C . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=65;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6905 . A G . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6911 . T C . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6917 . G A . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6920 . G A . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=47;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6923 . C T . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=44;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6931 . C A . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 6936 . C G . . DP=1;ECNT=8;MBQ=0,39;MFRL=0,162;MMQ=60,60;MPOS=31;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:6902_A_C:6902:0,0,0,1 +K03455 7441 . A ACCT . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=-2147483648;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7443 . A AGTG . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=94;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7449 . G A . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=100;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7452 . GGA G . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=103;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7455 . A ATG . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=106;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7457 . TGA T . . DP=1;ECNT=23;MBQ=0,39;MFRL=0,486;MMQ=60,60;MPOS=108;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7460 . CA C . . DP=1;ECNT=23;MBQ=0,37;MFRL=0,486;MMQ=60,60;MPOS=111;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,1:0.667:1:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,1 +K03455 7468 . CC TA . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=114;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7478 . C T . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=111;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7491 . A T . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=104;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7494 . A G . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=101;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7508 . GA AG . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=87;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7441_A_ACCT:7441:0,0,0,2 +K03455 7541 . C CGA . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=54;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7542 . AGT A . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=53;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7548 . C A . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=47;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7555 . GA AT . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=40;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7560 . TC GT . . DP=2;ECNT=23;MBQ=0,38;MFRL=0,586;MMQ=60,50;MPOS=35;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7568 . T C . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=-1073741804;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7571 . T C . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=24;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7581 . C A . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=14;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7584 . T C . . DP=2;ECNT=23;MBQ=0,39;MFRL=0,586;MMQ=60,50;MPOS=11;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7603 . A AGGG . . DP=2;ECNT=23;MBQ=0,37;MFRL=0,586;MMQ=60,50;MPOS=-8;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,2:0|1:7541_C_CGA:7541:0,0,0,2 +K03455 7604 . T G . . DP=2;ECNT=23;MBQ=0,33;MFRL=0,586;MMQ=60,50;MPOS=-22;POPAF=7.30;TLOD=8.70 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:0,2:0.667:2:0,0:0,1:0|1:7541_C_CGA:7541:0,0,0,2