Mercurial > repos > iuc > bcftools_plugin_setgt
diff test-data/concat.1.a.vcf @ 0:7e1a7520e05f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
| author | iuc |
|---|---|
| date | Wed, 06 Jul 2016 07:07:31 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/concat.1.a.vcf Wed Jul 06 07:07:31 2016 -0400 @@ -0,0 +1,32 @@ +##fileformat=VCFv4.0 +##FILTER=<ID=Fail,Description="Test"> +##FILTER=<ID=q10,Description="Quality below 10"> +##INFO=<ID=XX,Number=1,Type=Integer,Description="Test"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##contig=<ID=2,length=62435964> +##contig=<ID=1,length=62435964> +##samtoolsVersion=0.2.0-rc10+htslib-0.2.0-rc10 +##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 +##ALT=<ID=X,Description="Represents allele(s) other than observed."> +##bcftools_callVersion=0.2.0-rc10-2-gcd94fde+htslib-0.2.0-rc10 +##bcftools_callCommand=call -vm -f GQ -S mpileup.2014-07-03//pooled/1/1:1-1000000.samples - +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A +1 100 . GTTT G 1806 q10 XX=11;DP=35 GT:GQ:DP 0/1:409:35 +1 110 . C T,G 1792 Fail DP=32 GT:GQ:DP 0/1:245:32 +1 110 . CAAA C 1792 Fail DP=32 GT:GQ:DP 0/1:245:32 +1 120 . GA G 628 q10 DP=21 GT:GQ:DP 1/1:21:21 +1 130 . G T 1016 Fail DP=22 GT:GQ:DP 0/1:212:22 +1 130 . GAA GG 1016 Fail DP=22 GT:GQ:DP 0/1:212:22 +1 140 . GT G 727 PASS DP=30 GT:GQ:DP 0/1:150:30 +1 150 . TAAAA TA,T 246 Fail DP=10 GT:GQ:DP 1/2:12:10 +1 160 . TAAAA TA,T 246 Fail DP=10 GT:GQ:DP 1/2:12:10 +2 100 . GTTT G 1806 q10 DP=35 GT:GQ:DP 0/1:409:35 +2 110 . CAAA C 1792 PASS DP=32 GT:GQ:DP 0/1:245:32 +2 120 . GA G 628 q10 DP=21 GT:GQ:DP 1/1:21:21 +2 130 . GAA G 1016 PASS DP=22 GT:GQ:DP 0/1:212:22 +2 140 . GT G 727 PASS DP=30 GT:GQ:DP 0/1:150:30 +2 150 . TAAAA TA,T 246 PASS DP=10 GT:GQ:DP 1/2:12:10 +2 160 . TAAAA TA,TC,T 246 PASS DP=10 GT:GQ:DP 0/2:12:10