Mercurial > repos > iuc > bcftools_filter

annotate test-data/concat.1.a.vcf @ 13:abafcb875ba6 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 d5a01866d60f9775392420988259f1e79c464163"
author iuc
date Thu, 14 Oct 2021 10:08:42 +0000
parents 061729be105d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.0
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
2 ##FILTER=<ID=Fail,Description="Test">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
3 ##FILTER=<ID=q10,Description="Quality below 10">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
4 ##INFO=<ID=XX,Number=1,Type=Integer,Description="Test">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
5 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
7 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
8 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
9 ##contig=<ID=2,length=62435964>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
10 ##contig=<ID=1,length=62435964>
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
11 ##samtoolsVersion=0.2.0-rc10+htslib-0.2.0-rc10
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
12 ##samtoolsCommand=samtools mpileup -t INFO/DPR -C50 -pm3 -F0.2 -d10000 -ug -r 1:1-1000000 -b mpileup.2014-07-03//lists/chr1-pooled.list -f human_g1k_v37.fasta
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
13 ##ALT=<ID=X,Description="Represents allele(s) other than observed.">
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
14 ##bcftools_callVersion=0.2.0-rc10-2-gcd94fde+htslib-0.2.0-rc10
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
15 ##bcftools_callCommand=call -vm -f GQ -S mpileup.2014-07-03//pooled/1/1:1-1000000.samples -
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
16 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
17 1 100 . GTTT G 1806 q10 XX=11;DP=35 GT:GQ:DP 0/1:409:35
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
18 1 110 . C T,G 1792 Fail DP=32 GT:GQ:DP 0/1:245:32
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
19 1 110 . CAAA C 1792 Fail DP=32 GT:GQ:DP 0/1:245:32
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
20 1 120 . GA G 628 q10 DP=21 GT:GQ:DP 1/1:21:21
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
21 1 130 . G T 1016 Fail DP=22 GT:GQ:DP 0/1:212:22
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
22 1 130 . GAA GG 1016 Fail DP=22 GT:GQ:DP 0/1:212:22
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
23 1 140 . GT G 727 PASS DP=30 GT:GQ:DP 0/1:150:30
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
24 1 150 . TAAAA TA,T 246 Fail DP=10 GT:GQ:DP 1/2:12:10
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
25 1 160 . TAAAA TA,T 246 Fail DP=10 GT:GQ:DP 1/2:12:10
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
26 2 100 . GTTT G 1806 q10 DP=35 GT:GQ:DP 0/1:409:35
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
27 2 110 . CAAA C 1792 PASS DP=32 GT:GQ:DP 0/1:245:32
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
28 2 120 . GA G 628 q10 DP=21 GT:GQ:DP 1/1:21:21
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
29 2 130 . GAA G 1016 PASS DP=22 GT:GQ:DP 0/1:212:22
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
30 2 140 . GT G 727 PASS DP=30 GT:GQ:DP 0/1:150:30
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
31 2 150 . TAAAA TA,T 246 PASS DP=10 GT:GQ:DP 1/2:12:10
061729be105d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
32 2 160 . TAAAA TA,TC,T 246 PASS DP=10 GT:GQ:DP 0/2:12:10