annotate test-data/filter.3.vcf @ 2:039ea3f1dea9 draft

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

##fileformat=VCFv4.2
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=STR,Number=A,Type=String,Description="Testing string and Number=A in INFO">
##INFO=<ID=TXT0,Number=1,Type=String,Description="Testing in INFO">
##INFO=<ID=TXT,Number=.,Type=String,Description="Testing in INFO">
##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">
##SAMPLE=<ID=NORMAL,SampleName=B,Description="Less-than (\"<\") and greater-than (\">\") quoting nonsense where double brackets would do just fine",softwareName=<Nonsense,Software>,softwareVer=<119,65>,softwareParam=<.>,MetadataResource=http://somewhere.com/path>
##INFO=<ID=CIGAR,Number=A,Type=String,Description="test">
##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
##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=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
##FORMAT=<ID=STR,Number=1,Type=String,Description="Test">
##FILTER=<ID=q20,Description="Mapping quality below 20">
##contig=<ID=1,assembly=b37,length=249250621>
##contig=<ID=2,assembly=b37,length=243199373>
##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
##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	3162006	.	GAA	G,GA	238	q20	DP=19;AN=4;AC=1,1;XRF=1e6,2e6,3e6;XRI=1111,2222,3333;XRS=ABC,DEF,GHI;XAF=1e6,2e6;XAI=1111,2222;XAS=ABC,DEF;XGF=1e6,2e6,3e6,4e6,5e6,6e6;XGI=11,22,33,44,55,66;XGS=ABC,DEF,GHI,JKL,MNO,PQR;TXT=ABC,DEF,GHI	GT:GQ:DP:STR	0/1:589:19:XX	0/2:1:1:YY
1	3162007	.	TAGGG	CAGGG,CAGGT	238	q20	AO=52101,113;CIGAR=1X4M,1X3M1X;TXT0=text	GT:FGS:FGI:FGF:FAS:FAI:FAF:FRS:FRI:FRF	0/1:AAAAAA,BBBBB,CCCC,DDD,EE,F:1,2,3,4,5,6:1e-1,2e-2,3e-3,4e-4,5e-5,6e-6:AAA,B:1,2:1e-1,2e-2:A,BB,CCC:1,2,3:1e-1,2e-2,3e-3	2:AAAAAA,BBB,C:1,2,3:1e-1,2e-2,3e-3:AAA,B:1,2:1e-1,2e-2:A,BB,CCC:1,2,3:1e-1,2e-2,3e-3