Mercurial > repos > iuc > bcftools_query

annotate test-data/reheader.vcf @ 9:3d2e6a8a966c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
author iuc
date Mon, 29 Jul 2019 18:12:14 -0400
parents 2fea169065ec
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.1
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
3 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
4 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
5 ##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
6 ##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
7 ##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
8 ##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
9 ##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
10 ##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
11 ##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
12 ##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
13 ##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
14 ##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
15 ##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
16 ##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
17 ##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
18 ##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
19 ##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
20 ##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
21 ##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
22 ##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
23 ##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
24 ##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
25 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
26 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
27 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
28 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
29 ##contig=<ID=1,length=2147483647>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
30 ##contig=<ID=2,length=2147483647>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
31 ##contig=<ID=3,length=2147483647>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
32 ##contig=<ID=4,length=2147483647>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
33 ##contig=<ID=5,length=2147483647>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
34 ##contig=<ID=20,length=2147483647>
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
35 ##FILTER=<ID=Test,Description="Test Filter">
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
36 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
37 2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
38 2 114 . TC TTCC,TTC 999 PASS INDEL;AN=4;AC=2,2 GT:DP 1/2:1 1/2:1
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
39 2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
40 20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
41 20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
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
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
43 20 59 . AG . 999 PASS AN=4 GT:PL:DP 0/0:0:4 0/0:0:4
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
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
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
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
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
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
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
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
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
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
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
49 20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
50 20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
51 3 10 . GTGGAC GTGGACACAC,GTGGACAC,GTGGACACACAC,GTGG,GTGGACACACACAC,ATGGACACACAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
52 3 15 . CACA CAC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
53 4 21 . ATTTTTTTTTTTTTTTC ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0
2fea169065ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
54 5 22 . A AGA 999 PASS INDEL;AN=0 GT:DP ./.:0 ./.:0