Mercurial > repos > iuc > bcftools_plugin_missing2ref

comparison test-data/merge.2.a.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 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
5 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
7 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
8 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
9 ##FILTER=<ID=q10,Description="Quality below 10">
10 ##FILTER=<ID=test,Description="Testing filter">
11 ##contig=<ID=1,assembly=b37,length=249250621>
12 ##contig=<ID=2,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 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
21 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
22 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
23 1 3000000 . C CCG 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245
24 1 3000150 . C A 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245
25 1 3000151 . C A 59.2 PASS AN=4;AC=2 GT:DP:GQ 0/1:32:245 0/1:32:245
26 1 3106154 . C CC 342 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
27 1 3106154 . C A 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
28 1 3200000 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
29 1 3200010 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
30 1 3200020 . C G,T 59.2 PASS AN=4;AC=2 GT:GL ./.:1,2,3,4,5,6 .:1,2,3