annotate test-data/vcf/merlin.vcf @ 129:d08080933718 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6d8a6a308c219c112dbfc09fe48ad462746d6fb0

##fileformat=VCFv4.0
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=1000GenomesPilot-NCBI36
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number	of	Samples	With	Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total	Depth">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele	Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral	Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP	membership,	build	129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2	membership">
##FILTER=<ID=q10,Description="Quality	below	10">
##FILTER=<ID=s50,Description="Less	than	50%	of	samples	have	data">
##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=HQ,Number=2,Type=Integer,Description="Haplotype	Quality">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
Merlin	170	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
Merlin	1020	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3
Merlin	3445	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4
Merlin	5050	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
Merlin	20000	microsat1	GTCT	G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3