Mercurial > repos > iuc > bcftools_stats

comparison test-data/filter.1.vcf @ 0:92e47ae9a121 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 07:09:13 -0400
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-1:000000000000 0:92e47ae9a121
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 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
5 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
6 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
7 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
8 ##FILTER=<ID=q10,Description="Quality below 10">
9 ##test=<xx=A,yy=B,zz=C>
10 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
11 ##contig=<ID=1,assembly=b37,length=249250621>
12 ##contig=<ID=2,assembly=b37,length=249250621>
13 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
14 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
15 ##readme=AAAAAA
16 ##readme=BBBBBB
17 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A
18 1 1000 . G A 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
19 1 1001 . G A 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
20 1 1003 . GT G 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
21 1 1006 . G A 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
22 1 1007 . G A 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
23 1 2000 . T C 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
24 1 2001 . T C 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
25 1 2003 . T TC 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
26 1 2005 . T C 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
27 1 2006 . T C 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
28 2 1001 . GT G 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
29 2 1004 . GT G 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
30 2 1008 . GT G 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
31 2 2001 . A AT 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
32 2 2003 . A AT 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
33 2 2006 . A AT 1806 . DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20