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view test-data/output.vcf @ 2:98fe794d2ec0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 4255237ed7a51299e25bd7de7ad52ac5d419a56c
author iuc
date Sun, 04 Sep 2022 07:54:30 +0000
parents 7608209110d3
children 918c8b94c8d8
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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=1.4.0
##contig=<ID=K03455,length=9719>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR8525881
K03455	2652	.	G	A	24.2	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:24:201:0,200:0.995025:24,35,0
K03455	2660	.	T	C	21.9	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:21:213:0,213:1:21,30,0
K03455	2664	.	A	G	20.9	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:21:238:0,238:1:20,33,0
K03455	2669	.	G	A	16.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:16:258:0,250:0.968992:16,33,0
K03455	2720	.	T	C	34.9	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:35:384:0,380:0.989583:34,49,0
K03455	2797	.	G	A	38.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:37:669:0,666:0.995516:38,43,0
K03455	2848	.	T	TA	39.4	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:36:820:85,704:0.858537:39,39,0
K03455	2874	.	C	T	34.6	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:34:777:1,756:0.972973:34,46,0
K03455	2882	.	G	T	34.6	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:34:737:9,721:0.97829:34,47,0
K03455	2894	.	T	C	29.1	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:29:728:1,717:0.98489:29,51,0
K03455	2906	.	C	T	16	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:16:653:2,650:0.995406:15,33,0
K03455	2913	.	G	A	21.6	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:22:639:1,638:0.998435:21,40,0
K03455	2987	.	C	T	4.1	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:4:235:0,234:0.995745:1,21,0
K03455	3020	.	A	G	13.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:13:100:0,100:1:13,20,0
K03455	3042	.	A	C	0	RefCall	.	GT:GQ:DP:AD:VAF:PL	0/0:32:12:9,3:0.25:0,36,33