Mercurial > repos > iuc > gatk4_mutect2
diff test-data/Mutect2-out2.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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mutect2-out2.vcf Wed Oct 30 15:33:59 2019 -0400 @@ -0,0 +1,84 @@ +##fileformat=VCFv4.2 +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> +##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> +##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> +##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> +##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> +##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)"> +##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> +##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample SRR8525881 --output output.vcf --interval-set-rule UNION --interval-exclusion-padding 0 --input input.bam --read-validation-stringency SILENT --reference reference.fa --add-output-sam-program-record true --add-output-vcf-command-line true --verbosity ERROR --QUIET true --read-filter AmbiguousBaseReadFilter --read-filter FirstOfPairReadFilter --read-filter GoodCigarReadFilter --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-padding 0 --interval-merging-rule ALL --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --ambig-filter-frac 0.05 --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="October 29, 2019 1:14:20 PM EDT"> +##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> +##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> +##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants"> +##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> +##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> +##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality"> +##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> +##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor"> +##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup"> +##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes"> +##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> +##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals"> +##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles"> +##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact"> +##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> +##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> +##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors"> +##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> +##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact"> +##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors"> +##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing"> +##INFO=<ID=UNIQ_ALT_READ_COUNT,Number=1,Type=Integer,Description="Number of ALT reads with unique start and mate end positions at a variant site"> +##MutectVersion=2.2 +##contig=<ID=K03455,length=9719> +##filtering_status=Warning: unfiltered Mutect 2 calls. Please run FilterMutectCalls to remove false positives. +##source=Mutect2 +##tumor_sample=SRR8525881 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR8525881 +K03455 4861 . A G . . DP=1;ECNT=14;MBQ=0,37;MFRL=0,400;MMQ=60,60;MPOS=10;POPAF=7.30;TLOD=4.20 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,1:0.667:1:0,1:0,0:0,0,1,0 +K03455 4918 . G A . . DP=7;ECNT=14;MBQ=38,37;MFRL=303,370;MMQ=60,60;MPOS=19;POPAF=7.30;TLOD=8.65 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:3,3:0.499:6:2,0:1,2:2,1,0,3 +K03455 4923 . A G . . DP=8;ECNT=14;MBQ=0,33;MFRL=0,314;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=34.22 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,8:0.900:8:0,3:0,3:0,0,3,5 +K03455 4949 . G A . . DP=12;ECNT=14;MBQ=38,37;MFRL=285,264;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=27.49 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:5,7:0.573:12:2,2:1,4:0|1:4949_G_A:4949:2,3,2,5 +K03455 4952 . C T . . DP=13;ECNT=14;MBQ=36,37;MFRL=285,264;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=27.48 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:5,7:0.573:12:1,2:2,5:0|1:4949_G_A:4949:2,3,2,5 +K03455 4988 . T C . . DP=22;ECNT=14;MBQ=36,38;MFRL=285,278;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=14.99 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:17,5:0.250:22:5,2:8,2:6,11,3,2 +K03455 4991 . T C . . DP=22;ECNT=14;MBQ=37,28;MFRL=271,309;MMQ=60,60;MPOS=38;POPAF=7.30;TLOD=4.85 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:20,2:0.125:22:8,0:10,1:9,11,0,2 +K03455 4996 . AC GA . . DP=25;ECNT=14;MBQ=38,32;MFRL=285,203;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=5.72 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:21,3:0.152:24:6,1:10,1:8,13,1,2 +K03455 4997 . C T,A . . DP=25;ECNT=14;MBQ=38,37,38;MFRL=282,292,264;MMQ=60,60,60;MPOS=10,31;POPAF=7.30,7.30;TLOD=8.86,34.99 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:8,3,13:0.148,0.517:24:4,0,5:3,2,8:5,3,5,11 +K03455 5004 . G A . . DP=26;ECNT=14;MBQ=37,36;MFRL=262,288;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=4.21 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:24,2:0.107:26:7,1:13,1:8,16,1,1 +K03455 5015 . A G . . DP=34;ECNT=14;MBQ=38,38;MFRL=269,258;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=88.69 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:10,22:0.677:32:4,5:6,16:4,6,5,17 +K03455 5018 . A G . . DP=34;ECNT=14;MBQ=38,38;MFRL=262,261;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=11.32 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:30,4:0.139:34:9,0:15,4:10,20,0,4 +K03455 5027 . G A . . DP=37;ECNT=14;MBQ=37,38;MFRL=260,229;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=12.64 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:31,5:0.157:36:10,0:18,5:0|1:5027_G_A:5027:10,21,0,5 +K03455 5036 . G A . . DP=36;ECNT=14;MBQ=39,38;MFRL=256,229;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=12.71 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:30,5:0.162:35:9,0:18,4:0|1:5027_G_A:5027:10,20,0,5 +K03455 5076 . A G . . DP=37;ECNT=27;MBQ=38,37;MFRL=278,190;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=15.35 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:31,5:0.158:36:5,0:25,5:0|1:5076_A_G:5076:5,26,0,5 +K03455 5098 . A G . . DP=42;ECNT=27;MBQ=38,38;MFRL=190,292;MMQ=60,60;MPOS=34;POPAF=7.30;TLOD=126.26 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:7,32:0.804:39:0,4:7,22:0,7,4,28 +K03455 5099 . C T . . DP=42;ECNT=27;MBQ=38,37;MFRL=292,190;MMQ=60,60;MPOS=36;POPAF=7.30;TLOD=22.52 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:34,7:0.186:41:4,0:28,6:0|1:5076_A_G:5076:4,30,0,7 +K03455 5121 . C T . . DP=41;ECNT=27;MBQ=37,38;MFRL=257,205;MMQ=60,60;MPOS=26;POPAF=7.30;TLOD=24.97 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:33,8:0.209:41:3,1:28,6:3,30,1,7 +K03455 5130 . TG CA . . DP=38;ECNT=27;MBQ=38,38;MFRL=194,275;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=122.82 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:8,30:0.778:38:0,0:7,28:0,8,2,28 +K03455 5131 . G A . . DP=38;ECNT=27;MBQ=0,38;MFRL=0,205;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=23.77 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,8:0.932:8:0,1:0,6:0,0,1,7 +K03455 5133 . T C . . DP=36;ECNT=27;MBQ=38,36;MFRL=293,216;MMQ=60,60;MPOS=33;POPAF=7.30;TLOD=31.26 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:27,9:0.268:36:2,0:23,8:0|1:5133_T_C:5133:2,25,0,9 +K03455 5137 . GG AG,AA . . DP=35;ECNT=27;MBQ=39,39,39;MFRL=194,216,337;MMQ=60,60,60;MPOS=34,28;POPAF=7.30,7.30;TLOD=31.44,66.06 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:8,9,18:0.270,0.495:35:0,0,1:7,8,16:0,8,1,26 +K03455 5146 . AGG A . . DP=33;ECNT=27;MBQ=38,38;MFRL=315,216;MMQ=60,60;MPOS=43;POPAF=7.30;RPA=4,2;RU=G;STR;TLOD=31.38 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:24,9:0.286:33:1,0:22,9:0|1:5133_T_C:5133:1,23,0,9 +K03455 5147 . G A . . DP=33;ECNT=27;MBQ=38,37;MFRL=181,343;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=66.04 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:7,17:0.694:24:0,0:6,13:0|1:5147_G_A:5147:0,7,1,16 +K03455 5153 . GGTTT G . . DP=29;ECNT=27;MBQ=38,38;MFRL=296,216;MMQ=60,60;MPOS=50;POPAF=7.30;TLOD=32.02 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:20,9:0.323:29:0,0:19,9:0|1:5133_T_C:5133:0,20,0,9 +K03455 5155 . T C . . DP=28;ECNT=27;MBQ=38,38;MFRL=169,331;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=49.64 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:6,13:0.669:19:0,0:6,12:0|1:5147_G_A:5147:0,6,0,13 +K03455 5156 . T A . . DP=28;ECNT=27;MBQ=38,37;MFRL=315,181;MMQ=60,60;MPOS=15;POPAF=7.30;TLOD=16.29 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:14,5:0.283:19:0,0:14,5:0|1:5156_T_A:5156:0,14,0,5 +K03455 5157 . T G . . DP=28;ECNT=27;MBQ=38,37;MFRL=181,331;MMQ=60,60;MPOS=54;POPAF=7.30;TLOD=49.65 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,13:0.703:18:0,0:5,13:0,5,0,13 +K03455 5169 . C T . . DP=20;ECNT=27;MBQ=39,39;MFRL=296,170;MMQ=60,60;MPOS=37;POPAF=7.30;TLOD=20.02 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:14,6:0.318:20:0,0:14,6:0,14,0,6 +K03455 5175 . A T . . DP=19;ECNT=27;MBQ=37,39;MFRL=203,299;MMQ=60,60;MPOS=55;POPAF=7.30;TLOD=34.23 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:10,9:0.476:19:0,0:9,9:0|1:5147_G_A:5147:0,10,0,9 +K03455 5177 . G C . . DP=18;ECNT=27;MBQ=39,37;MFRL=299,216;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=25.72 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:11,7:0.400:18:0,0:10,7:0|1:5133_T_C:5133:0,11,0,7 +K03455 5179 . CC AC,AA . . DP=17;ECNT=27;MBQ=39,36,39;MFRL=366,216,315;MMQ=60,60,60;MPOS=60,51;POPAF=7.30,7.30;TLOD=26.12,30.50 GT:AD:AF:DP:F1R2:F2R1:SB 0/1/2:2,7,8:0.400,0.450:17:0,0,0:2,7,8:0,2,0,15 +K03455 5189 . G A . . DP=18;ECNT=27;MBQ=39,39;MFRL=203,315;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=30.08 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:10,8:0.450:18:1,0:9,8:1,9,0,8 +K03455 5190 . A G . . DP=18;ECNT=27;MBQ=39,20;MFRL=293,181;MMQ=60,60;MPOS=62;POPAF=7.30;TLOD=9.31 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:15,3:0.200:18:0,0:15,2:0|1:5156_T_A:5156:0,15,1,2 +K03455 5196 . T C . . DP=18;ECNT=27;MBQ=39,37;MFRL=293,181;MMQ=60,60;MPOS=56;POPAF=7.30;TLOD=9.19 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:15,3:0.200:18:0,1:15,2:0,15,1,2 +K03455 5220 . G A . . DP=16;ECNT=27;MBQ=38,38;MFRL=312,219;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=21.54 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:10,6:0.389:16:1,0:9,6:0|1:5220_G_A:5220:1,9,0,6 +K03455 5223 . T A . . DP=16;ECNT=27;MBQ=37,39;MFRL=293,181;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=9.40 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:13,3:0.222:16:0,1:13,2:0|1:5223_T_A:5223:0,13,1,2 +K03455 5230 . T C . . DP=16;ECNT=27;MBQ=38,39;MFRL=293,181;MMQ=60,60;MPOS=22;POPAF=7.30;TLOD=9.40 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:13,3:0.222:16:0,1:12,2:0|1:5223_T_A:5223:0,13,1,2 +K03455 5233 . G A . . DP=12;ECNT=27;MBQ=38,38;MFRL=293,216;MMQ=60,60;MPOS=11;POPAF=7.30;TLOD=18.49 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB 0|1:7,5:0.429:12:0,0:6,5:0|1:5220_G_A:5220:1,6,0,5 +K03455 5236 . A G . . DP=12;ECNT=27;MBQ=37,38;MFRL=216,256;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=22.57 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:5,6:0.539:11:0,1:5,5:0,5,1,5 +K03455 5240 . C T . . DP=11;ECNT=27;MBQ=37,37;MFRL=219,162;MMQ=60,60;MPOS=-1;POPAF=7.30;TLOD=9.66 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:8,3:0.308:11:0,0:7,3:1,7,0,3