Mercurial > repos > iuc > bcftools_plugin_missing2ref

comparison test-data/merge.c.vcf @ 0:5e9cf5308e97 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 07:07:16 -0400
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-1:000000000000 0:5e9cf5308e97
1 ##fileformat=VCFv4.1
2 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
3 ##INFO=<ID=TXT,Number=.,Type=String,Description="Testing in INFO">
4 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
5 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
6 ##INFO=<ID=INTA,Number=A,Type=Integer,Description="Testing Number=A in INFO">
7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
8 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
9 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
10 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
11 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
12 ##FILTER=<ID=q10,Description="Quality below 10">
13 ##FILTER=<ID=test,Description="Testing filter">
14 ##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
15 ##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
16 ##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
17 ##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
18 ##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
19 ##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
20 ##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
21 ##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
22 ##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
23 ##contig=<ID=1,assembly=b37,length=249250621>
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 ##readme=AAAAAA
28 ##readme=BBBBBB
29 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
30 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
31 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT C D
32 1 3062915 id3D GTTT G 48.7 q10 TXT=BB;DP=999;DP4=4,3,2,1;AN=4;AC=2 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20
33 1 3062915 idSNP G C,T 419 test TEST=5;DP4=1,2,3,4;AN=4;AC=1,1;INTA=1,2 GT:TT:GQ:DP:GL 0/1:0,1:409:35:-20,-5,-20,-20,-5,-20 0/2:0,1:409:35:-20,-5,-20,-20,-5,-20
34 1 3062915 id2D GTT G 999 q10 DP4=1,2,3,4;AN=4;AC=2 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20
35 1 3106154 . CAAA C 72.6 PASS AN=0;AC=0 GT:GQ:DP .:245:32 ./.:245:32
36 1 3106154 . C CT 459 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
37 1 3157410 . G T 46.7 q10 AN=4;AC=4 GT:GQ:DP 1/1:21:21 1/1:21:21
38 1 3162006 . GAA GA 206 PASS AN=4;AC=2;XRF=1e6,5e5;XRI=1111,5555;XRS=AAA,DDD;XAF=5e5;XAI=5555;XAS=DDD;XGF=1e6,5e5,9e9;XGI=1111,5555,9999;XGS=A,E,F GT:GQ:DP 0/1:212:22 0/1:212:22
39 1 3177144 . G . 364 PASS AN=4;AC=0 GT:GQ:DP 0/0:150:30 0/0:150:30
40 1 3184885 . TAAAA TA,T 8.42 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:12:10 1/2:12:10
41 2 3199812 . G GTT,GT 291 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26
42 3 3212016 . CTT C,CT 52.5 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:91:26
43 4 3258448 . TACACACAC T . PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31