Mercurial > repos > jjohnson > bcftools_plugin_missing2ref

comparison test-data/isec.b.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=q20,Description="Mapping quality below 20">
9 ##contig=<ID=1,assembly=b37,length=249250621>
10 ##contig=<ID=2,assembly=b37,length=243199373>
11 ##contig=<ID=3,assembly=b37,length=198022430>
12 ##contig=<ID=4,assembly=b37,length=191154276>
13 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
14 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
15 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
16 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT B
17 1 3062915 . G A 376 q20 DP=14;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:376:14:-10,0,-10
18 1 3062915 . GTTT GT 376 q20 DP=14;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:376:14:-10,0,-10
19 1 3106154 . C T 677 PASS DP=15;AN=2;AC=1 GT:GQ:DP:GL 0/1:277:15:-10,0,-10
20 1 3106154 . CAAAA C 677 PASS DP=15;AN=2;AC=1 GT:GQ:DP:GL 0/1:277:15:-10,0,-10
21 1 3157410 . GA G 249 PASS DP=11;AN=2;AC=1 GT:GQ:DP 0/1:49:11
22 1 3162006 . GAA G 663 PASS DP=19;AN=2;AC=1 GT:GQ:DP 0/1:589:19
23 1 3177144 . GT G 460 PASS DP=24;AN=2;AC=1 GT:GQ:DP 0/1:236:24
24 1 3184885 . TAAA T 598 PASS DP=16;AN=2;AC=1 GT:GQ:DP 0/1:435:16
25 2 3188209 . GA G 162 . DP=15;AN=2;AC=1 GT:GQ:DP 0/1:162:15
26 3 3199812 . G GTT,GT 353 PASS DP=19;AN=2;AC=1,1 GT:GQ:DP 1/2:188:19
27 4 3212016 . CTT C 677 q20 DP=15;AN=2;AC=1 GT:GQ:DP 0/1:158:15