annotate test-data/merge.c.vcf @ 14:912a8ff07fc9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"

##fileformat=VCFv4.1
##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
##INFO=<ID=TXT,Number=.,Type=String,Description="Testing in INFO">
##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">
##INFO=<ID=INTA,Number=A,Type=Integer,Description="Testing Number=A in INFO">
##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">
##INFO=<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">
##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
##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	C	D
1	3062915	id3D	GTTT	G	48.7	q10	TXT=BB;DP=999;DP4=4,3,2,1;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	C,T	419	test	TEST=5;DP4=1,2,3,4;AN=4;AC=1,1;INTA=1,2	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	3062915	id2D	GTT	G	999	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	3106154	.	CAAA	C	72.6	PASS	AN=0;AC=0	GT:GQ:DP	.:245:32	./.:245:32
1	3106154	.	C	CT	459	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
1	3157410	.	G	T	46.7	q10	AN=4;AC=4	GT:GQ:DP	1/1:21:21	1/1:21:21
1	3162006	.	GAA	GA	206	PASS	AN=4;AC=2;XRF=1e6,5e5;XRI=1111,5555;XRS=AAA,DDD;XAF=5e5;XAI=5555;XAS=DDD;XGF=1e6,5e5,9e9;XGI=1111,5555,9999;XGS=A,E,F	GT:GQ:DP	0/1:212:22	0/1:212:22
1	3177144	.	G	.	364	PASS	AN=4;AC=0	GT:GQ:DP	0/0:150:30	0/0:150:30
1	3184885	.	TAAAA	TA,T	8.42	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:12:10	1/2:12:10
2	3199812	.	G	GTT,GT	291	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:322:26	1/2:322:26
3	3212016	.	CTT	C,CT	52.5	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:91:26	1/2:91:26
4	3258448	.	TACACACAC	T	.	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31