Mercurial > repos > jjohnson > bcftools_plugin_missing2ref

comparison test-data/isec.a.vcf @ 0:ff65d6e0809b 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 20:51:04 -0400
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-1:000000000000 0:ff65d6e0809b
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 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
12 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
13 ##readme=AAAAAA
14 ##readme=BBBBBB
15 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A
16 1 3062915 . GTTT G 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
17 1 3062915 . G T 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20
18 1 3106154 . CAAA C 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32
19 1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32
20 1 3157410 . GA G 628 q10 DP=21;AN=2;AC=2 GT:GQ:DP 1/1:21:21
21 1 3162006 . GAA G 1016 PASS DP=22;AN=2;AC=1 GT:GQ:DP 0/1:212:22
22 1 3177144 . GT G 727 PASS DP=30;AN=2;AC=1 GT:GQ:DP 0/1:150:30
23 1 3184885 . TAAAA TA,T 246 PASS DP=10;AN=2;AC=1,1 GT:GQ:DP 1/2:12:10
24 2 3199812 . G GTT,GT 481 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:322:26
25 3 3212016 . CTT C,CT 565 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:91:26
26 4 3212016 . TACACACAC T 325 PASS DP=31;AN=2;AC=1 GT:GQ:DP 0/1:325:31
27 4 3258448 . TACACACAC T 325 PASS DP=31;AN=2;AC=1 GT:GQ:DP 0/1:325:31