Mercurial > repos > iuc > bcftools_merge

comparison test-data/filter.3.vcf @ 0:5add48c63b9a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:04:14 -0400
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-1:000000000000 0:5add48c63b9a
1 ##fileformat=VCFv4.2
2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
3 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
4 ##INFO=<ID=STR,Number=A,Type=String,Description="Testing string and Number=A in INFO">
5 ##INFO=<ID=TXT0,Number=1,Type=String,Description="Testing in INFO">
6 ##INFO=<ID=TXT,Number=.,Type=String,Description="Testing in INFO">
7 ##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
8 ##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
9 ##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
10 ##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
11 ##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
12 ##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
13 ##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
14 ##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
15 ##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
16 ##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>
17 ##INFO=<ID=CIGAR,Number=A,Type=String,Description="test">
18 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
19 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
20 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
21 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
22 ##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
23 ##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
24 ##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
25 ##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
26 ##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
27 ##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
28 ##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
29 ##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
30 ##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
31 ##FORMAT=<ID=STR,Number=1,Type=String,Description="Test">
32 ##FILTER=<ID=q20,Description="Mapping quality below 20">
33 ##contig=<ID=1,assembly=b37,length=249250621>
34 ##contig=<ID=2,assembly=b37,length=243199373>
35 ##contig=<ID=3,assembly=b37,length=198022430>
36 ##contig=<ID=4,assembly=b37,length=191154276>
37 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
38 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
39 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
40 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
41 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
42 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