Mercurial > repos > iuc > bcftools_plugin_counts

comparison test-data/norm.vcf @ 0:06cd2a0252dc 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 07:04:58 -0400
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-1:000000000000 0:06cd2a0252dc
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=3,length=2147483647>
10 ##contig=<ID=4,length=2147483647>
11 ##contig=<ID=5,length=2147483647>
12 ##contig=<ID=20,length=2147483647>
13 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
14 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
15 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
16 ##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
17 ##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
18 ##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
19 ##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
20 ##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
21 ##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
22 ##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
23 ##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
24 ##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
25 ##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
26 ##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
27 ##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
28 ##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
29 ##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
30 ##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
31 ##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
32 ##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
33 ##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
34 ##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
35 ##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
36 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002
37 1 105 . TAAACCCTAAA TAA,TAACCCTAAA 999 PASS INDEL;AN=4;AC=2,2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06,500000;XRI=1111,2222,5555;XRS=AAA,BBB,DDD;XAF=1e+06,500000;XAI=1111,5555;XAS=AAA,DDD;XGF=1e+06,2e+06,3e+06,500000,.,9e+09;XGI=1111,2222,3333,5555,.,9999;XGS=A,B,C,E,.,F GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS 1/2:1,2,3,4,5,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF 1/2:1,2,3,4,5,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,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,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1
41 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1
42 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1
43 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0
44 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
45 20 59 . AG . 999 PASS AN=4 GT:PL:DP 0/0:0:4 0/0:0:4
46 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
47 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
48 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
49 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
50 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
51 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
52 20 275 . A C,G 999 PASS INDEL;AN=2;AC=0,2 GT:PL:DP:FGF:FGI:FGS:FSTR 2:0,0,0:0:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC:WORD 2:0,0,0:0:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC:WORD
53 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
54 3 10 . GTGGAC GTGGACACAC,GTGGACAC,GTGGACACACAC,GTGG,GTGGACACACACAC,ATGGACACACAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0
55 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0
56 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0
57 5 22 . A AGA 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0