Mercurial > repos > devteam > vcfannotategenotypes
diff test-data/vcfannotategenotypes-test1.vcf @ 0:7a32e4b43579 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotategenotypes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
| author | devteam |
|---|---|
| date | Mon, 09 Nov 2015 12:29:39 -0500 |
| parents | |
| children | 9c9969071728 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfannotategenotypes-test1.vcf Mon Nov 09 12:29:39 2015 -0500 @@ -0,0 +1,33 @@ +##fileformat=VCFv4.0 +##fileDate=20090805 +##source=myImputationProgramV3.1 +##reference=1000GenomesPilot-NCBI36 +##phasing=partial +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> +##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency"> +##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> +##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"> +##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> +##FILTER=<ID=q10,Description="Quality below 10"> +##FILTER=<ID=s50,Description="Less than 50% of samples have data"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> +##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element"> +##ALT=<ID=CNV,Description="Copy number variable region"> +##INFO=<ID=added-genotypes.has_variant,Number=0,Type=Flag,Description="True if added-genotypes has a called alternate among samples under comparison."> +##FORMAT=<ID=added-genotypes,Number=1,Type=String,Description="Genotype from added-genotypes."> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . added-genotypes.has_variant GT:HQ:added-genotypes 0|0:10,10:0/0 0|0:10,10:./. 0/1:3,3:0/1 +19 112 . A G 10 . added-genotypes.has_variant GT:HQ:added-genotypes 0|0:10,10:0/0 0|0:10,10:./. 0/1:3,3:0/1 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:48:1:51,51:0/0 1|0:48:8:51,51:./. 1/1:43:5:.,.:1/1 +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:49:3:58,50:0/0 0|1:3:5:65,3:./. 0/0:41:3:.,.:0/0 +20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 1|2:21:6:23,27:1/2 2|1:2:0:18,2:./. 2/2:35:4:.,.:2/2 +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3;added-genotypes.has_variant GT:GQ:DP:HQ:added-genotypes 0|0:54:.:56,60:0/0 0|0:48:4:51,51:./. 0/0:61:2:.,.:0/0 +20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3;added-genotypes.has_variant GT:GQ:DP:added-genotypes 0/1:.:4:0/1 0/2:17:2:./. 1/1:40:3:1/1 +20 1235237 . T . 0 . added-genotypes.has_variant GT:added-genotypes 0/0:0/0 0|0:./. . +X 10 rsTest AC A,ATG 10 PASS added-genotypes.has_variant GT:added-genotypes 0:0 0/1:./. 0|2:0/2