Mercurial > repos > iuc > bcftools_plugin_setgt

annotate test-data/concat.1.b.vcf @ 20:681bdf1e22ff 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 bfc4ff4956b94885638ae07a2560bac5f84fcca8
author iuc
date Tue, 16 Jul 2024 17:11:40 +0000
parents 7e1a7520e05f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.0
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
2 ##samtoolsVersion=0.2.0-rc10+htslib-0.2.0-rc10
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
3 ##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
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
4 ##ALT=<ID=X,Description="Represents allele(s) other than observed.">
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
5 ##bcftools_callVersion=0.2.0-rc10-2-gcd94fde+htslib-0.2.0-rc10
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
6 ##bcftools_callCommand=call -vm -f GQ -S mpileup.2014-07-03//pooled/1/1:1-1000000.samples -
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
7 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
7e1a7520e05f 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">
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
9 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
10 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
11 ##FILTER=<ID=q10,Description="Quality below 10">
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
12 ##contig=<ID=3,length=62435964>
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
13 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
14 3 142 . GTTT G 1806 q10 DP=35 GT:GQ:DP 0/1:409:35
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
15 3 152 . CAAA C 1792 PASS DP=32 GT:GQ:DP 0/1:245:32
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
16 3 162 . GA G 628 q10 DP=21 GT:GQ:DP 1/1:21:21
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
17 3 172 . GAA G 1016 PASS DP=22 GT:GQ:DP 0/1:212:22
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
18 3 182 . GT G 727 PASS DP=30 GT:GQ:DP 0/1:150:30
7e1a7520e05f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
19 3 192 . TAAAA TA,T 246 PASS DP=10 GT:GQ:DP 1/2:12:10