Mercurial > repos > jjohnson > bcftools_convert_from_vcf

comparison test-data/annots.vcf @ 0:d396503fdbdb 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 20:47:20 -0400
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-1:000000000000 0:d396503fdbdb
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 ##test=<ID=4,IE=5>
16 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
17 ##readme=AAAAAA
18 ##readme=BBBBBB
19 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
20 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
21 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
22 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
23 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
24 1 3000150 id1 C T 99 PASS STR=id1;AN=4;AC=0 GT:GQ 0|0:999 0|0:999
25 1 3000151 id2 C T 99 PASS STR=id2;AN=4;AC=0 GT:DP:GQ 0|0:99:999 0|0:99:999
26 1 3062915 idIndel GTTT G 99 PASS DP4=1,2,3,4;AN=4;AC=0;INDEL;STR=testIndel GT:GQ:DP:GL 0|0:999:99:-99,-9,-99 0|0:999:99:-99,-9,-99
27 1 3062915 idSNP G T,C 99 PASS STR=testSNP;TEST=5;DP4=1,2,3,4;AN=3;AC=0,0 GT:TT:GQ:DP:GL 0|0:9,9:999:99:-99,-9,-99,-99,-9,-99 0:9,9:999:99:-99,-9,-99
28 1 3106154 id4 CAAA C 99 PASS STR=id4;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99
29 1 3106154 id5 C CT 99 PASS STR=id5;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99
30 1 3157410 id6 GA GC,G 99 PASS STR=id6;AN=4;AC=0 GT:GQ:DP 0|0:99:99 0|0:99:99
31 1 3162006 id7 GAA GG 99 PASS STR=id7;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99
32 1 3177144 id8 G T 99 PASS STR=id8;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99
33 1 3177144 id9 G . 99 PASS STR=id9;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99
34 1 3184885 id10 TAAAA TA,T 99 PASS STR=id10;AN=4;AC=0,0 GT:GQ:DP 0|0:99:99 0|0:99:99
35 2 3199812 id11 G GTT,GT 99 PASS STR=id11;AN=4;AC=0,0 GT:GQ:DP 0|0:999:99 0|0:999:99
36 3 3212016 id12 CTT C,CT 99 PASS STR=id12;AN=4;AC=0,0 GT:GQ:DP 0|0:99:99 0|0:99:99
37 4 3258448 id13 TACACACAC T 99 PASS STR=id13;AN=4;AC=0 GT:GQ:DP 0|0:999:99 0|0:999:99