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view test-data/output.vcf @ 0:7608209110d3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
author iuc
date Mon, 06 Sep 2021 17:34:08 +0000
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children 98fe794d2ec0
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=RefCall,Description="Genotyping model thinks this site is reference.">
##FILTER=<ID=LowQual,Description="Confidence in this variant being real is below calling threshold.">
##FILTER=<ID=NoCall,Description="Site has depth=0 resulting in no call.">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position (for use with symbolic alleles)">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block.">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele">
##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.2.0
##contig=<ID=K03455,length=9719>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR8525881
K03455	2652	.	G	A	23.7	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:24:201:0,200:0.995025:23,45,0
K03455	2660	.	T	C	25.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:25:213:0,213:1:25,45,0
K03455	2664	.	A	G	21.4	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:21:238:0,238:1:21,45,0
K03455	2669	.	G	A	20.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:20:258:0,250:0.968992:20,43,0
K03455	2720	.	T	C	31.9	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:32:384:0,380:0.989583:31,47,0
K03455	2797	.	G	A	39.4	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:39:669:0,666:0.995516:39,54,0
K03455	2848	.	T	TA	41.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:39:820:85,704:0.858537:41,43,0
K03455	2874	.	C	T	32	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:32:777:1,756:0.972973:32,45,0
K03455	2882	.	G	T	33.2	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:33:737:9,721:0.97829:33,49,0
K03455	2894	.	T	C	28.2	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:28:728:1,717:0.98489:28,51,0
K03455	2906	.	C	T	23.7	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:24:653:2,650:0.995406:23,53,0
K03455	2913	.	G	A	27.4	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:27:639:1,638:0.998435:27,53,0
K03455	2987	.	C	T	16.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:16:235:0,234:0.995745:16,38,0
K03455	3020	.	A	G	3.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:3:100:0,100:1:0,24,0
K03455	3042	.	A	C	0	RefCall	.	GT:GQ:DP:AD:VAF:PL	0/0:37:12:9,3:0.25:0,40,39