Mercurial > repos > jjohnson > bcftools_convert_from_vcf

view test-data/concat.1.a.vcf @ 1:00c4dab57376 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:33:34 -0400
parents d396503fdbdb
children
line wrap: on
line source

##fileformat=VCFv4.0
##FILTER=<ID=Fail,Description="Test">
##FILTER=<ID=q10,Description="Quality below 10">
##INFO=<ID=XX,Number=1,Type=Integer,Description="Test">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=2,length=62435964>
##contig=<ID=1,length=62435964>
##samtoolsVersion=0.2.0-rc10+htslib-0.2.0-rc10
##samtoolsCommand=samtools mpileup -t INFO/DPR -C50 -pm3 -F0.2 -d10000 -ug -r 1:1-1000000 -b mpileup.2014-07-03//lists/chr1-pooled.list -f human_g1k_v37.fasta
##ALT=<ID=X,Description="Represents allele(s) other than observed.">
##bcftools_callVersion=0.2.0-rc10-2-gcd94fde+htslib-0.2.0-rc10
##bcftools_callCommand=call -vm -f GQ -S mpileup.2014-07-03//pooled/1/1:1-1000000.samples -
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
1	100	.	GTTT	G	1806	q10	XX=11;DP=35	GT:GQ:DP	0/1:409:35
1	110	.	C	T,G	1792	Fail	DP=32	GT:GQ:DP	0/1:245:32
1	110	.	CAAA	C	1792	Fail	DP=32	GT:GQ:DP	0/1:245:32
1	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
1	130	.	G	T	1016	Fail	DP=22	GT:GQ:DP	0/1:212:22
1	130	.	GAA	GG	1016	Fail	DP=22	GT:GQ:DP	0/1:212:22
1	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
1	150	.	TAAAA	TA,T	246	Fail	DP=10	GT:GQ:DP	1/2:12:10
1	160	.	TAAAA	TA,T	246	Fail	DP=10	GT:GQ:DP	1/2:12:10
2	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
2	110	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
2	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
2	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
2	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
2	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
2	160	.	TAAAA	TA,TC,T	246	PASS	DP=10	GT:GQ:DP	0/2:12:10