Mercurial > repos > jjohnson > bcftools_plugin_missing2ref

comparison test-data/check.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=TEST,Number=1,Type=Integer,Description="Testing Tag">
3 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
4 ##INFO=<ID=DP,Number=1,Type=Integer,Description="read depth">
5 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
7 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
8 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
9 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
10 ##FILTER=<ID=q10,Description="Quality below 10">
11 ##FILTER=<ID=test,Description="Testing filter">
12 ##contig=<ID=1,assembly=b37,length=249250621>
13 ##contig=<ID=3,assembly=b37,length=198022430>
14 ##contig=<ID=4,assembly=b37,length=191154276>
15 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
16 ##readme=AAAAAA
17 ##readme=BBBBBB
18 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
19 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
20 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
21 1 3062915 id3D GTTT G 12.9 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
22 1 3062915 idSNP G T,C 12.6 test TEST=5;DP4=1,2,3,4;AN=4;AC=1,1 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
23 1 3106154 . CAAA C 342 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
24 1 3106154 . G A 59.2 PASS AN=4;AC=1 GT:GQ:DP 0/1:245:32 0/0:245:32
25 1 3157410 . G A 90.6 q10 AN=4;AC=4 GT:GQ:DP 1/1:21:21 1/1:21:21
26 1 3162006 . G A 60.2 PASS AN=4;AC=3 GT:GQ:DP 1/1:212:22 0/1:212:22
27 1 3177144 . GT G 45 PASS AN=4;AC=2 GT:GQ:DP 0/1:150:30 0/1:150:30
28 1 3184885 . TAAAA TA,T 61.5 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:12:10 1/2:12:10
29 2 3199812 . G GTT,GT 82.7 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26
30 3 3212016 . CTT C,CT 79 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:91:26
31 4 3258448 . TACACACAC T 59.9 PASS DP=62;AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
32 4 3258449 . GCAAA GA,G 59.9 PASS DP=62;AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
33 4 3258450 . AAAAGAAAAAG A,AAAAAAG 59.9 PASS DP=60;AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
34 4 3258451 . AAA AGT 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
35 4 3258452 . AAA AGA 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
36 4 3258453 . AACA AGA 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
37 4 3258453 . ACA AAGA 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31
38 4 3258454 . AACA AACA 59.9 PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31