view test-data/populations/populations.snps.vcf @ 0:45385ba40a75 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 11:03:22 -0400
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##fileformat=VCFv4.2
##fileDate=20190617
##source="Stacks v2.4"
##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allele Depth">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=loc_strand,Number=1,Type=Character,Description="Genomic strand the corresponding Stacks locus aligns on">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	PopA_01	PopA_02
1	34	.	A	C	.	PASS	NS=2;AF=0.500	GT:DP:AD:GQ:GL	0/1:18:9,9:40:-20.07,0.00,-20.07	0/1:12:6,6:40:-13.54,-0.00,-13.54
1	89	.	A	C	.	PASS	NS=2;AF=0.500	GT:DP:AD:GQ:GL	0/1:18:9,9:40:-20.07,0.00,-20.07	0/1:12:6,6:40:-13.54,-0.00,-13.54
2	145	.	C	T	.	PASS	NS=2;AF=0.500	GT:DP:AD:GQ:GL	0/1:17:9,8:40:-17.57,0.00,-20.29	0/1:13:5,8:40:-18.77,-0.00,-10.39
2	157	.	G	T	.	PASS	NS=2;AF=0.500	GT:DP:AD:GQ:GL	0/1:17:9,8:40:-17.57,0.00,-20.29	0/1:13:5,8:40:-18.77,-0.00,-10.39
3	163	.	G	A	.	PASS	NS=2;AF=0.250	GT:DP:AD:GQ:GL	0/0:23:23,0:40:-0.00,-6.89,-68.45	0/1:23:11,12:40:-28.67,0.00,-25.99
3	182	.	G	A	.	PASS	NS=2;AF=0.250	GT:DP:AD:GQ:GL	0/0:23:23,0:40:-0.00,-6.89,-68.45	0/1:23:11,12:40:-28.67,0.00,-25.99