Mercurial > repos > iuc > bcftools_query_list_samples

diff test-data/concat.1.a.vcf @ 0:1af52ffc90e3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:08:29 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/concat.1.a.vcf	Wed Jul 06 07:08:29 2016 -0400
@@ -0,0 +1,32 @@
+##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