Mercurial > repos > iuc > bcftools_filter
annotate test-data/concat.1.b.vcf @ 18:277719af4dd7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit cdb4558db96dd58f9f85267488a1e27ad813fca4
author | iuc |
---|---|
date | Thu, 29 Sep 2022 09:02:19 +0000 |
parents | 061729be105d |
children |
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 ##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
|
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 |
061729be105d
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."> |
061729be105d
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 |
061729be105d
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 - |
061729be105d
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"> |
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 ##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
|
10 ##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
|
11 ##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
|
12 ##contig=<ID=3,length=62435964> |
061729be105d
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 |
061729be105d
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 |
061729be105d
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 |
061729be105d
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 |
061729be105d
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 |
061729be105d
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 |
061729be105d
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 |