Mercurial > repos > jjohnson > bcftools_convert_from_vcf

comparison test-data/reheader.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=DP,Number=1,Type=Integer,Description="Total Depth">
3 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
4 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
5 ##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
6 ##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
7 ##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
8 ##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
9 ##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
10 ##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
11 ##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
12 ##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
13 ##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
14 ##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
15 ##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
16 ##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
17 ##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
18 ##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
19 ##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
20 ##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
21 ##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
22 ##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
23 ##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
24 ##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
25 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
26 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
27 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
28 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
29 ##contig=<ID=1,length=2147483647>
30 ##contig=<ID=2,length=2147483647>
31 ##contig=<ID=3,length=2147483647>
32 ##contig=<ID=4,length=2147483647>
33 ##contig=<ID=5,length=2147483647>
34 ##contig=<ID=20,length=2147483647>
35 ##FILTER=<ID=Test,Description="Test Filter">
36 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002
37 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1
38 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1
39 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1
40 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1
41 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0
42 20 5 . TGGG TAC,TG,TGGGG,AC . PASS INDEL;AN=4;AC=2,2,0,0 GT:PL:DP 1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1 1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1
43 20 59 . AG . 999 PASS AN=4 GT:PL:DP 0/0:0:4 0/0:0:4
44 20 80 . CACAG CACAT 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
45 20 81 . A C 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
46 20 95 . TCACCG ACACCG 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
47 20 95 . TCACCG AAAAAA 999 Test AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
48 20 273 . CAAAAAAAAAAAAAAAAAAAAA CAAAAAAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=4;AC=2,2 GT:PL:DP 1/2:0,3,5,3,5,5:1 1/2:0,3,5,3,5,5:1
49 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
50 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
51 3 10 . GTGGAC GTGGACACAC,GTGGACAC,GTGGACACACAC,GTGG,GTGGACACACACAC,ATGGACACACAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0
52 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0
53 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0
54 5 22 . A AGA 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0