Mercurial > repos > iuc > bcftools_norm
annotate test-data/concat.1.a.vcf @ 13:c077f71d351f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
author | iuc |
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date | Fri, 05 Feb 2021 19:18:28 +0000 |
parents | e9555e894608 |
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rev | line source |
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e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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1 ##fileformat=VCFv4.0 |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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2 ##FILTER=<ID=Fail,Description="Test"> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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3 ##FILTER=<ID=q10,Description="Quality below 10"> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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4 ##INFO=<ID=XX,Number=1,Type=Integer,Description="Test"> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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5 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> |
e9555e894608
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"> |
e9555e894608
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"> |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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9 ##contig=<ID=2,length=62435964> |
e9555e894608
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> |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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."> |
e9555e894608
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 |
e9555e894608
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 - |
e9555e894608
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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16 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |
e9555e894608
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 |