annotate test-data/filter.2.vcf @ 2:cf06b44624c7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69

##fileformat=VCFv4.1
##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
##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">
##FILTER=<ID=test,Description="Testing filter">
##contig=<ID=1,assembly=b37,length=249250621>
##contig=<ID=2,assembly=b37,length=249250621>
##contig=<ID=3,assembly=b37,length=198022430>
##contig=<ID=4,assembly=b37,length=191154276>
##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
##readme=AAAAAA
##readme=BBBBBB
##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">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
1	3000150	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
1	3000151	.	C	T	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
1	3062915	id3D	GTTT	G	12.9	q10	DP4=1,2,3,4;AN=4;AC=2;INDEL;STR=test	GT:GQ:DP:GL	0/1:25:35:-20,-5,-20	0/1:45:11:-20,-5,-20
1	3062915	idSNP	G	T,C	12.6	test	TEST=5;DP4=1,2,3,4;AN=3;AC=1,1	GT:TT:GQ:DP:GL	0/1:0,1:409:35:-20,-5,-20,-20,-5,-20	2:0,1:409:35:-20,-5,-20
1	3106154	.	CAAA	C	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:25:300
1	3106154	.	C	CT	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:25:12	0/1:245:310
1	3157410	.	GA	G	90.6	q10	AN=4;AC=4	GT:GQ:DP	1/1:21:21	1/1:21:21
1	3162006	.	GAA	G	60.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:212:22	0/1:212:22
1	3177144	.	G	T	45	PASS	AN=4;AC=2	GT:GQ:DP	0/0:150:30	1/1:150:30
1	3177144	.	G	.	45	PASS	AN=4;AC=0	GT:GQ:DP	0/0:150:30	0/0:150:30
1	3184885	.	TAAAA	TA,T	61.5	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:12:10	1/2:12:20
2	3199812	.	G	GTT,GT	82.7	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:322:20	1/2:322:10
3	3212016	.	CTT	C,CT	79	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:91:26	1/2:91:26
4	3258448	.	TACACACAC	T	59.9	PASS	AN=4;AC=2	GT	0/1	0/1