Mercurial > repos > jjohnson > bcftools_filter

comparison test-data/merge.b.vcf @ 0:442f9d982db3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:47:47 -0400
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-1:000000000000 0:442f9d982db3
1 ##fileformat=VCFv4.1
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=1,Type=String,Description="Testing string and Number=A in INFO">
5 ##INFO=<ID=TXT,Number=.,Type=String,Description="Testing in INFO">
6 ##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
7 ##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
8 ##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
9 ##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
10 ##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
11 ##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
12 ##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
13 ##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
14 ##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
15 ##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>
16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
17 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
19 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
20 ##FORMAT=<ID=STR,Number=1,Type=String,Description="Testing string in format">
21 ##FILTER=<ID=q20,Description="Mapping quality below 20">
22 ##contig=<ID=1,assembly=b37,length=249250621>
23 ##contig=<ID=2,assembly=b37,length=243199373>
24 ##contig=<ID=3,assembly=b37,length=198022430>
25 ##contig=<ID=4,assembly=b37,length=191154276>
26 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
27 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
28 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
29 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT B
30 1 3062915 idSNP G A 24.6 q20 DP=14;DP4=1,2,3,4;AN=2;STR=.;AC=1 GT:GQ:DP:STR:GL 0/1:376:14:ABC:-10,0,-10
31 1 3062915 id1D GTT GT 101 q20 DP=14;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL:STR 0/1:376:14:-10,0,-10:DEF
32 1 3062915 id3D GTTT G 84.6 q20 TXT=AA;DP=14;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:376:14:-10,0,-10
33 1 3106154 . C T 999 PASS DP=15;AN=2;AC=1 GT:GQ:DP:GL 0/1:277:15:-10,0,-10
34 1 3106154 . CAAAA C 15.4 PASS DP=15;AN=2;AC=1 GT:GQ:DP:GL 0/1:277:15:-10,0,-10
35 1 3157410 . GAC G 36.8 PASS DP=11;AN=2;AC=1 GT:GQ:DP 0/1:49:11
36 1 3162006 . GAA G 238 PASS DP=19;AN=2;AC=1;XRF=1e6,2e6;XRI=1111,2222;XRS=AAA,BBB;XAF=1e6;XAI=1111;XAS=AAA;XGF=1e6,2e6,3e6;XGI=1111,2222,3333;XGS=A,B,C GT:GQ:DP 0/1:589:19
37 1 3177144 . G T 999 PASS DP=24;AN=2;AC=1 GT:GQ:DP 0/1:236:24
38 1 3177144 . GT G 999 PASS DP=24;AN=2;AC=1 GT:GQ:DP 0/1:236:24
39 1 3184885 . TAAA T 25.8 PASS DP=16;AN=2;AC=1 GT:GQ:DP 0/1:435:16
40 2 3188209 . GA G 41.5 . DP=15;AN=2;AC=1 GT:GQ:DP 0/1:162:15
41 3 3199812 . GA GTT,GT 17.5 PASS DP=19;AN=2;AC=1,1 GT:GQ:DP 1/2:188:19
42 4 3212016 . CTT C 999 q20 DP=15;AN=2;AC=1 GT:GQ:DP 0/1:158:15