annotate test-data/check.vcf @ 0:2a6c13f8cc5a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e

##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=DP,Number=1,Type=Integer,Description="read depth">
##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=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">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
1	3062915	id3D	GTTT	G	12.9	q10	DP4=1,2,3,4;AN=4;AC=2	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
1	3062915	idSNP	G	T,C	12.6	test	TEST=5;DP4=1,2,3,4;AN=4;AC=1,1	GT:TT:GQ:DP:GL	0/1:0,1:409:35:-20,-5,-20,-20,-5,-20	0/2:0,1:409:35:-20,-5,-20,-20,-5,-20
1	3106154	.	CAAA	C	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
1	3106154	.	G	A	59.2	PASS	AN=4;AC=1	GT:GQ:DP	0/1:245:32	0/0:245:32
1	3157410	.	G	A	90.6	q10	AN=4;AC=4	GT:GQ:DP	1/1:21:21	1/1:21:21
1	3162006	.	G	A	60.2	PASS	AN=4;AC=3	GT:GQ:DP	1/1:212:22	0/1:212:22
1	3177144	.	GT	G	45	PASS	AN=4;AC=2	GT:GQ:DP	0/1:150:30	0/1:150:30
1	3184885	.	TAAAA	TA,T	61.5	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:12:10	1/2:12:10
2	3199812	.	G	GTT,GT	82.7	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:322:26	1/2:322:26
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	DP=62;AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
4	3258449	.	GCAAA	GA,G	59.9	PASS	DP=62;AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
4	3258450	.	AAAAGAAAAAG	A,AAAAAAG	59.9	PASS	DP=60;AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
4	3258451	.	AAA	AGT	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
4	3258452	.	AAA	AGA	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
4	3258453	.	AACA	AGA	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
4	3258453	.	ACA	AAGA	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
4	3258454	.	AACA	AACA	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31