Mercurial > repos > anton > vcfbreakcreatemulti
diff test-data/vcfbreakcreatemulti-test2-input.vcf @ 0:c0387293312e
Imported from capsule None
| author | anton |
|---|---|
| date | Wed, 11 Jun 2014 17:11:07 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcfbreakcreatemulti-test2-input.vcf Wed Jun 11 17:11:07 2014 -0400 @@ -0,0 +1,34 @@ +##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"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 +19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 +20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. +20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. +20 1110696 rs6040355 A G 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ ./1:21:6:23,27 ./1:2:0:18,2 ./.:35:4:.,. +20 1110696 rs6040355 A T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ ./1:21:6:23,27 ./1:2:0:18,2 1/1:35:4:.,. +20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. +20 1234567 microsat1 G GA 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 ./0:17:2 1/1:40:3 +20 1234567 microsat1 G GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP ./0:.:4 0/1:17:2 ./.:40:3 +20 1235237 . T . 0 . . GT 0/0 0|0 . +X 10 rsTest AC A 10 PASS . GT 0 0/1 ./0 +X 10 rsTest AC ATG 10 PASS . GT 0 ./0 0/1