annotate test-data/Mutect2-out3.vcf @ 1:fd2d6e035c3f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516"

##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  --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --tumor-sample SRR8525881 --af-of-alleles-not-in-resource -1.0 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --normal-lod 2.2 --base-quality-score-threshold 18 --native-pair-hmm-threads 1 --min-base-quality-score 10 --output output.vcf --max-reads-per-alignment-start 50 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --input input.bam --read-validation-stringency SILENT --reference reference.fa --add-output-sam-program-record true --add-output-vcf-command-line true --verbosity ERROR --QUIET true --gcs-max-retries 20 --annotation StrandBiasBySample --annotation BaseQualityHistogram --annotation OrientationBiasReadCounts --annotation-group StandardMutectAnnotation  --genotype-pon-sites false --genotype-germline-sites false --mitochondria-mode false --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --use-jdk-deflater false --use-jdk-inflater false --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.0",Date="November 15, 2019 4:25:49 PM EST">
##INFO=<ID=BQHIST,Number=A,Type=Integer,Description="Base quality counts for each allele represented sparsely as alternating entries of qualities and counts for each allele.For example [10,1,0,20,0,1] means one ref base with quality 10 and one alt base with quality 20.">
##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##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	2652	.	G	A	.	.	BQHIST=16,1,0,18,9,0,20,25,0,29,5,0,32,20,0,33,12,0,34,2,0,37,27,0,38,13,0,39,13,0;DP=129;ECNT=6;MBQ=0,33;MFRL=0,273;MMQ=60,60;MPOS=5;POPAF=7.30;TLOD=571.21	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,129:0.992:129:0,57:0,60:0|1:2652_G_A:2652:0,0,115,14
K03455	2660	.	T	C	.	.	BQHIST=15,1,0,16,1,0,17,2,0,20,24,0,29,1,0,32,4,0,33,3,0,34,2,0,35,6,0,37,48,0,38,27,0,39,20,0;DP=162;ECNT=6;MBQ=0,37;MFRL=0,274;MMQ=60,60;MPOS=13;POPAF=7.30;TLOD=717.35	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,162:0.993:162:0,66:0,69:0|1:2652_G_A:2652:0,0,145,17
K03455	2664	.	A	G	.	.	BQHIST=18,0,2,19,0,2,20,0,27,30,0,3,32,0,15,33,0,13,34,0,1,35,0,4,36,0,1,37,0,17,38,0,65,39,0,13;DP=165;ECNT=6;MBQ=0,37;MFRL=0,273;MMQ=60,60;MPOS=14;POPAF=7.30;TLOD=572.42	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,165:0.993:165:0,80:0,79:0,0,148,17
K03455	2669	.	G	A	.	.	BQHIST=16,1,0,18,1,0,19,2,0,20,32,0,29,1,0,32,5,0,33,8,0,34,3,0,36,1,0,37,45,0,38,44,0,39,31,0;DP=177;ECNT=6;MBQ=0,37;MFRL=0,274;MMQ=60,60;MPOS=17;POPAF=7.30;TLOD=755.51	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,174:0.994:174:0,84:0,86:0|1:2652_G_A:2652:0,0,155,19
K03455	2677	.	A	G	.	.	BQHIST=15,3,0,17,1,0,18,1,0,19,4,0,20,35,2,33,6,0,34,9,0,36,2,0,37,29,0,38,36,0,39,55,2;DP=186;ECNT=6;MBQ=38,30;MFRL=273,240;MMQ=60,60;MPOS=30;POPAF=7.30;TLOD=5.37	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:181,4:0.024:185:83,2:89,2:162,19,3,1
K03455	2720	.	T	C	.	.	BQHIST=14,3,0,16,10,0,17,1,0,18,20,0,20,65,0,30,1,0,32,2,0,33,25,0,34,9,0,36,12,0,37,81,0,38,24,0,39,40,0;DP=339;ECNT=6;MBQ=0,36;MFRL=0,263;MMQ=60,60;MPOS=51;POPAF=7.30;TLOD=1040.98	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,295:0.996:295:0,120:0,139:0,0,250,45
K03455	2797	.	G	A	.	.	BQHIST=15,2,0,16,3,0,17,1,0,18,22,0,20,188,0,32,5,0,33,21,0,35,8,0,36,8,0,37,56,0,38,62,0,39,110,0;DP=521;ECNT=12;MBQ=0,35;MFRL=0,246;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=1710.50	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,497:0.998:497:0,245:0,213:0,0,334,163
K03455	2831	.	A	T	.	.	BQHIST=14,5,0,15,12,0,16,2,1,17,48,3,18,12,10,19,3,0,20,138,0,29,2,0,30,5,1,31,6,0,32,9,0,33,40,2,34,14,0,35,1,0,36,6,0,37,52,0,38,43,0,39,102,0;DP=534;ECNT=12;MBQ=33,18;MFRL=240,262;MMQ=60,60;MPOS=23;POPAF=7.30;TLOD=4.34	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:502,17:0.023:519:221,1:197,2:298,204,0,17
K03455	2848	.	T	TA	.	.	BQHIST=14,0,2,15,0,18,16,0,11,17,0,1,20,6,241,27,0,1,29,0,1,30,1,14,31,0,1,32,0,13,33,2,22,34,0,11,35,0,1,36,0,20,37,0,47,38,1,71,39,3,81;DP=596;ECNT=12;MBQ=30,30;MFRL=257,246;MMQ=60,60;MPOS=32;POPAF=7.30;RPA=6,7;RU=A;STR;TLOD=1256.09	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:13,560:0.982:573:6,264:7,260:8,5,299,261
K03455	2849	.	A	AG	.	.	BQHIST=14,0,8,15,0,1,16,0,2,17,0,1,18,0,16,19,1,0,20,2,269,27,0,1,29,0,2,30,1,8,31,0,2,32,0,4,33,0,17,34,1,6,35,0,4,36,0,33,37,1,38,38,0,100,39,2,62;DP=594;ECNT=12;MBQ=20,32;MFRL=245,276;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=3.21	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:577,8:0.012:585:285,2:261,5:309,268,4,4
K03455	2872	.	T	A	.	.	BQHIST=14,1,2,15,2,0,16,0,10,17,6,6,18,15,51,19,0,38,20,0,164,27,1,1,29,0,16,30,0,3,31,0,9,32,0,20,33,0,29,34,0,12,35,0,12,36,0,9,37,0,78,38,0,46,39,0,53;DP=620;ECNT=12;MBQ=29,18;MFRL=240,283;MMQ=60,60;MPOS=29;POPAF=7.30;TLOD=3.49	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:559,25:0.023:584:222,1:230,0:259,300,25,0
K03455	2874	.	C	T	.	.	BQHIST=16,0,6,17,1,5,18,0,53,19,0,13,20,0,199,29,0,4,30,0,2,31,0,11,32,0,31,33,0,40,34,0,13,35,0,12,36,0,11,37,0,85,38,0,53,39,0,50;DP=598;ECNT=12;MBQ=17,32;MFRL=360,241;MMQ=60,60;MPOS=32;POPAF=7.30;TLOD=2009.02	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:1,595:0.997:596:0,262:0,249:1,0,292,303
K03455	2882	.	G	T	.	.	BQHIST=14,1,0,16,5,0,17,7,0,18,21,0,19,12,0,20,194,0,29,2,0,30,4,0,31,4,1,32,3,0,33,25,0,34,1,0,35,19,0,36,11,0,37,82,0,38,50,0,39,111,0;DP=569;ECNT=12;MBQ=31,33;MFRL=360,246;MMQ=60,60;MPOS=40;POPAF=7.30;TLOD=1892.82	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:1,568:0.997:569:1,254:0,252:1,0,287,281
K03455	2889	.	G	A	.	.	BQHIST=14,0,11,15,0,1,16,0,4,17,0,4,18,0,13,19,0,17,20,0,189,29,0,1,30,0,3,31,0,1,32,0,7,33,2,31,34,1,4,35,0,9,36,0,14,37,1,76,38,1,70,39,2,94,40,0,1;DP=568;ECNT=12;MBQ=33,37;MFRL=249,308;MMQ=60,60;MPOS=53;POPAF=7.30;TLOD=8.92	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:552,7:0.016:559:244,4:256,3:282,270,6,1
K03455	2891	.	A	G	.	.	BQHIST=14,0,1,16,4,0,17,9,0,18,18,0,19,8,0,20,176,6,30,1,0,31,4,0,32,7,0,33,25,1,34,2,0,35,26,0,36,7,1,37,75,0,38,84,0,39,87,0;DP=564;ECNT=12;MBQ=35,20;MFRL=249,231;MMQ=60,60;MPOS=45;POPAF=7.30;TLOD=8.84	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:543,9:0.013:552:237,4:257,4:276,267,5,4
K03455	2894	.	T	C	.	.	BQHIST=14,1,0,15,5,0,16,4,0,17,13,0,18,32,0,19,4,0,20,160,0,27,1,0,29,3,0,30,5,0,32,5,0,33,24,0,34,12,0,35,5,0,36,8,0,37,81,0,38,68,0,39,113,0;DP=551;ECNT=12;MBQ=0,35;MFRL=0,250;MMQ=60,60;MPOS=41;POPAF=7.30;TLOD=1769.47	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,551:0.998:551:0,236:0,249:0,0,280,271
K03455	2906	.	C	T	.	.	BQHIST=16,0,2,18,0,4,19,0,10,20,0,144,30,0,2,31,0,1,32,0,3,33,0,19,34,0,3,35,0,19,36,0,11,37,0,57,38,0,75,39,0,145;DP=495;ECNT=12;MBQ=0,37;MFRL=0,250;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2348.23	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,495:0.998:495:0,225:0,254:0|1:2906_C_T:2906:0,0,235,260
K03455	2913	.	G	A	.	.	BQHIST=18,4,0,19,5,0,20,132,0,29,1,0,30,2,0,31,2,0,32,2,0,33,17,0,34,1,0,35,4,0,36,1,0,37,62,0,38,65,0,39,182,0,40,4,0;DP=492;ECNT=12;MBQ=0,38;MFRL=0,251;MMQ=60,60;MPOS=42;POPAF=7.30;TLOD=2341.59	GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB	0|1:0,492:0.998:492:0,224:0,251:0|1:2906_C_T:2906:0,0,234,258
K03455	2987	.	C	T	.	.	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=847.14	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,219:0.995:219:0,99:0,103:0,0,86,133
K03455	2992	.	T	G	.	.	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=3.86	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:179,9:0.043:188:74,2:77,0:74,105,9,0
K03455	3016	.	C	A	.	.	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	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:88,7:0.081:95:24,1:34,0:61,27,7,0
K03455	3020	.	A	G	.	.	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	GT:AD:AF:DP:F1R2:F2R1:SB	0/1:0,90:0.989:90:0,32:0,43:0,0,65,25