Mercurial > repos > jjohnson > bcftools_plugin_missing2ref

comparison test-data/norm.merge.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=VCFv4.2
2 ##FILTER=<ID=PASS,Description="All filters passed">
3 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
4 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
5 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
6 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
7 ##contig=<ID=1,length=2147483647>
8 ##contig=<ID=2,length=2147483647>
9 ##contig=<ID=20,length=2147483647>
10 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
11 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
12 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
13 ##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
14 ##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
15 ##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
16 ##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
17 ##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
18 ##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
19 ##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
20 ##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
21 ##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
22 ##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
23 ##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
24 ##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
25 ##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
26 ##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
27 ##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
28 ##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
29 ##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
30 ##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
31 ##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
32 ##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
33 ##FILTER=<ID=FAIL1,Description="Failed filter 1">
34 ##FILTER=<ID=FAIL2,Description="Failed filter 2">
35 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002
36 1 105 . TAAACCCTAAA TAA 999 PASS INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06;XRI=1111,2222;XRS=AAA,BBB;XAF=1e+06;XAI=1111;XAS=AAA;XGF=1e+06,2e+06,3e+06;XGI=1111,2222,3333;XGS=A,B,C GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS 1/0:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC 1/0:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC
37 1 105 . TAAACCCTAAA TAACCCTAAA 999 PASS INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,500000;XRI=1111,5555;XRS=AAA,DDD;XAF=500000;XAI=5555;XAS=DDD;XGF=1e+06,500000,9e+09;XGI=1111,5555,9999;XGS=A,E,F GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS 0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF 0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF
38 2 1 . GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTATTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCT ACGT 999 PASS INDEL;AN=4;AC=2 GT:DP 1/0:1 1/0:1
39 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1
40 2 114 . TC TTCC 999 FAIL1 INDEL;AN=4;AC=2 GT:DP 1/0:1 1/0:1
41 2 114 . TC TTC 999 PASS INDEL;AN=4;AC=2 GT:DP 0/1:1 0/1:1
42 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1
43 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1
44 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0
45 20 5 . TGGG TAC . PASS INDEL;AN=4;AC=2 GT:PL:DP 1/0:1,2,3:1 1/0:1,2,3:1
46 20 5 id0001 TGGG TG . PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:1,4,6:1 0/1:1,4,6:1
47 20 5 id0002 TGGG TGGGG . PASS INDEL;AN=4;AC=0 GT:PL:DP 0/0:1,7,10:1 0/0:1,7,10:1
48 20 5 . TGGG AC . PASS INDEL;AN=4;AC=0 GT:PL:DP 0/0:1,11,15:1 0/0:1,11,15:1
49 20 59 id0003 AG . 999 PASS AN=4 GT:PL:DP 0/0:0:4 0/0:0:4
50 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
51 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
52 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
53 20 95 . TCACCG AAAAAA 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
54 20 273 . CAAAAAAAAAAAAAAAAAAAAA CAAAAAAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=4;AC=2 GT:PL:DP 1/0:0,3,5:1 1/0:0,3,5:1
55 20 273 . CAAAAAAAAAAAAAAAAAAAAA CAAAAAAAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:0,3,5:1 0/1:0,3,5:1
56 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
57 20 275 . A C 0 FAIL1 INDEL;AN=2;AC=0 GT:PL:DP:FGF:FGI:FGS:FSTR 0:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD 0:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD
58 20 275 . A G 0 FAIL2 INDEL;AN=2;AC=2 GT:PL:DP:FGF:FGI:FGS:FSTR 1:0,0:0:1e+06,3e+06:1111,3333:A,CCC:WORD 1:0,0:0:1e+06,3e+06:1111,3333:A,CCC:WORD
59 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
60 20 300 . A C 998 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
61 20 300 . A G 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0