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view test-data/output.g.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
parents
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	1	.	T	<*>	0	.	END=1000	GT:GQ:MIN_DP:PL	0/0:1:0:0,0,0
K03455	1001	.	G	<*>	0	.	END=2000	GT:GQ:MIN_DP:PL	0/0:1:0:0,0,0
K03455	2001	.	T	<*>	0	.	END=2597	GT:GQ:MIN_DP:PL	0/0:1:0:0,0,0
K03455	2598	.	G	<*>	0	.	END=2598	GT:GQ:MIN_DP:PL	./.:0:2:59,6,0
K03455	2599	.	A	<*>	0	.	END=2603	GT:GQ:MIN_DP:PL	0/0:6:2:0,6,59
K03455	2604	.	CCA	C,<*>	5.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:5:2:0,2,0:1,0:3,15,0,990,990,990
K03455	2607	.	A	<*>	0	.	END=2607	GT:GQ:MIN_DP:PL	0/0:6:2:0,6,59
K03455	2608	.	A	T,<*>	7.8	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:7:2:0,2,0:1,0:6,14,0,990,990,990
K03455	2609	.	A	T,<*>	4.8	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:4:2:0,2,0:1,0:2,14,0,990,990,990
K03455	2610	.	G	<*>	0	.	END=2612	GT:GQ:MIN_DP:PL	0/0:6:2:0,6,59
K03455	2613	.	A	T,<*>	1.1	RefCall	.	GT:GQ:DP:AD:VAF:PL	./.:7:2:0,2,0:1,0:0,19,5,990,990,990
K03455	2614	.	A	<*>	0	.	END=2614	GT:GQ:MIN_DP:PL	0/0:6:2:0,6,59
K03455	2615	.	A	<*>	0	.	END=2615	GT:GQ:MIN_DP:PL	0/0:15:5:0,15,149
K03455	2616	.	C	<*>	0	.	END=2616	GT:GQ:MIN_DP:PL	./.:0:7:8,0,158
K03455	2617	.	A	<*>	0	.	END=2617	GT:GQ:MIN_DP:PL	./.:0:6:11,0,131
K03455	2618	.	A	<*>	0	.	END=2618	GT:GQ:MIN_DP:PL	0/0:18:6:0,18,179
K03455	2619	.	T	<*>	0	.	END=2619	GT:GQ:MIN_DP:PL	0/0:21:7:0,21,209
K03455	2620	.	G	<*>	0	.	END=2620	GT:GQ:MIN_DP:PL	0/0:39:13:0,39,389
K03455	2621	.	G	<*>	0	.	END=2651	GT:GQ:MIN_DP:PL	0/0:50:49:0,147,1469
K03455	2652	.	G	A,<*>	20.1	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:20:201:0,201,0:1,0:20,47,0,990,990,990
K03455	2653	.	T	<*>	0	.	END=2659	GT:GQ:MIN_DP:PL	0/0:50:201:0,300,2999
K03455	2660	.	T	C,<*>	25.5	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:25:213:0,213,0:1,0:25,45,0,990,990,990
K03455	2661	.	T	<*>	0	.	END=2663	GT:GQ:MIN_DP:PL	0/0:50:213:0,300,2999
K03455	2664	.	A	G,<*>	21.3	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:21:238:0,238,0:1,0:21,45,0,990,990,990
K03455	2665	.	C	<*>	0	.	END=2668	GT:GQ:MIN_DP:PL	0/0:50:240:0,300,2999
K03455	2669	.	G	A,<*>	20.6	PASS	.	GT:GQ:DP:AD:VAF:PL	1/1:21:250:0,250,0:1,0:20,42,0,990,990,990