Mercurial > repos > iuc > bcftools_plugin_missing2ref

view test-data/isec.a.vcf @ 7:31c096c6b156 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author iuc
date Thu, 21 Feb 2019 16:02:30 -0500
parents 5e9cf5308e97
children
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##fileformat=VCFv4.1
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
##FILTER=<ID=q10,Description="Quality below 10">
##test=<xx=A,yy=B,zz=C>
##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##readme=AAAAAA
##readme=BBBBBB
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
1	3062915	.	GTTT	G	1806	q10	DP=35;DP4=1,2,3,4;AN=2;AC=1	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20
1	3062915	.	G	T	1806	q10	DP=35;DP4=1,2,3,4;AN=2;AC=1	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20
1	3106154	.	CAAA	C	1792	PASS	DP=32;AN=2;AC=1	GT:GQ:DP	0/1:245:32
1	3106154	.	C	T,CT	1792	PASS	DP=32;AN=2;AC=1	GT:GQ:DP	0/1:245:32
1	3157410	.	GA	G	628	q10	DP=21;AN=2;AC=2	GT:GQ:DP	1/1:21:21
1	3162006	.	GAA	G	1016	PASS	DP=22;AN=2;AC=1	GT:GQ:DP	0/1:212:22
1	3177144	.	GT	G	727	PASS	DP=30;AN=2;AC=1	GT:GQ:DP	0/1:150:30
1	3184885	.	TAAAA	TA,T	246	PASS	DP=10;AN=2;AC=1,1	GT:GQ:DP	1/2:12:10
2	3199812	.	G	GTT,GT	481	PASS	DP=26;AN=2;AC=1,1	GT:GQ:DP	1/2:322:26
3	3212016	.	CTT	C,CT	565	PASS	DP=26;AN=2;AC=1,1	GT:GQ:DP	1/2:91:26
4	3212016	.	TACACACAC	T	325	PASS	DP=31;AN=2;AC=1	GT:GQ:DP	0/1:325:31
4	3258448	.	TACACACAC	T	325	PASS	DP=31;AN=2;AC=1	GT:GQ:DP	0/1:325:31