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view test-data/output.vcf @ 3:918c8b94c8d8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
author iuc
date Mon, 10 Apr 2023 11:11:16 +0000
parents 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=1.5.0
##contig=<ID=K03455,length=9719>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR8525881
K03455	2652	.	G	A	27.7	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:27:201:0,200:0.995025:27,33,0
K03455	2660	.	T	C	30.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:29:213:0,213:1:30,34,0
K03455	2664	.	A	G	24.1	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:24:238:0,238:1:24,32,0
K03455	2669	.	G	A	29.8	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:29:258:0,250:0.968992:29,36,0
K03455	2720	.	T	C	42.1	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:37:384:0,380:0.989583:42,38,0
K03455	2797	.	G	A	44.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:42:669:0,666:0.995516:44,46,0
K03455	2848	.	T	TA	46.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:38:820:85,704:0.858537:46,38,0
K03455	2874	.	C	T	36.2	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:32:777:1,756:0.972973:36,34,0
K03455	2882	.	G	T	37.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:33:737:9,721:0.97829:37,34,0
K03455	2894	.	T	C	32.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:30:728:1,717:0.98489:32,34,0
K03455	2906	.	C	T	32.2	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:29:653:2,650:0.995406:32,31,0
K03455	2913	.	G	A	41.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:39:639:1,638:0.998435:41,42,0
K03455	2987	.	C	T	11.7	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:11:235:0,234:0.995745:11,23,0
K03455	3020	.	A	G	0.8	RefCall	.	GT:GQ:DP:AD:VAF:PL	./.:8:100:0,100:1:0,26,7
K03455	3042	.	A	C	0	RefCall	.	GT:GQ:DP:AD:VAF:PL	0/0:37:12:9,3:0.25:0,41,39