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test_file.vcf
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test_file.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=18,length=80373285,assembly=B36,species="Homo sapiens",taxonomy=x>
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,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">
##FORMAT=<ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 and 1/1">
##FORMAT=<ID=HDS,Number=2,Type=Float,Description="Haplotype Dosages">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 NA00004 NA00005 NA00006
18 2234668 . G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 1|0:1,0:48:1:51,51 0|0:0,0:48:8:51,51 0/1:0,1:43:5:.,. 0/1:0,1:35:4:. 0/0:0,0:17:2:. 1/0:1,0:40:3:.
18 2234679 . G T 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 0|0:0,0:48:1:51,51 0|0:0,0:48:8:51,51 1/0:1,0:43:5:.,. 0/1:0,1:35:4:. 0/1:0,1:17:2:. 0/1:0,1:40:3:.
18 2234687 . G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 0|0:0,0:48:1:51,51 0|0:0,0:48:8:51,51 0/0:0,0:43:5:.,. 1/0:1,0:35:4:. 0/0:0,0:17:2:. 0/0:0,0:40:3:.
18 2234697 . T A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 1|0:1,0:48:1:51,51 0|0:0,0:48:8:51,51 1/0:1,0:43:5:.,. 0/0:0,0:35:4:. 0/0:0,0:17:2:. 0/0:0,0:40:3:.
18 2234767 . T G 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 0|0:0,0:48:1:51,51 1|0:1,0:48:8:51,51 0/1:0,1:43:5:.,. 0/1:0,1:35:4:. 0/0:0,0:17:2:. 1/1:1,0.9:40:3:.
20 14360 . G AC 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:GP 0|0:0,0:48:1:0.999,0.001,0 0|0:0,0:48:8:1,0,0 1/1:1,1:43:5:0,0.2,0.8 0/1:0,1:35:4:0.05,0.95,0 1/1:1,1:17:2:0,0,1 0/0:0,0:40:3:0.8,0.05,0.15
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 0|0:0,0:48:1:51,51 1|0:1,0:48:8:51,51 ./1:.,1:43:5:.,. 0/1:0,1:35:4:. 1/1:1,1:17:2:. 1/1:1,1:40:3:.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:HDS:GQ:DP:HQ 0|0:0,0:49:3:58,50 0|1:0,1:3:5:65,3 0/0:0,0:41:3:. 0/1:0,1:35:4:. 0/1:0,1:17:2:. 1/1:1,1:40:3:.
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:. 0/1:35:4:. 0/1:17:2:. 1/1:40:3:.
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:HDS:GQ:DP:HQ 0|0:0,0:54:7:56,60 0|0:0,0:48:4:51,51 0/0:0,0:61:2:. 0/1:0,1:35:4:. 0/1:0,1:17:2:. 1/1:1,1:40:3:.
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/0:40:3 2/1:35:4 1/2:17:2 1/1:40:3
20 1234667 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 0|0:0,0:48:1:51,51 1|0:1,0:48:8:51,51 ./1:.,1:43:5:.,. 0/1:0,1:35:4:. 1/1:1,1:17:2:. 1/1:1,1:40:3:.
20 1234767 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:HDS:GQ:DP:HQ 0|0:0,0:49:3:58,50 0|1:0,1:3:5:65,3 0/0:0,0:41:3:. 0/1:0,1:35:4:. 0/1:0,1:17:2:. 0/0:0,0:40:3:.
20 2230237 . T . 47 PASS NS=3;DP=13;AA=T GT:HDS:GQ:DP:HQ 0|0:0,0:54:7:56,60 1|0:1,0:48:4:51,51 0/0:0,0:61:2:. 1/0:1,0:35:4:. 0/1:0,1:17:2:. 1/1:1,1:40:3:.
20 2234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 2/1:35:4 1/2:17:2 1/0:40:3
20 3234687 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 1|0:1,0:48:1:51,51 1|0:1,0:48:8:51,51 0/0:0,0:43:5:.,. 1/0:1,0:35:4:. 0/0:0,0:17:2:. 0/0:0,0:40:3:.
20 3234697 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 1|0:1,0:48:1:51,51 1|0:1,0:48:8:51,51 1/0:1,0:43:5:.,. 0/0:0,0:35:4:. 0/0:0,0:17:2:. 0/0:0,0:40:3:.
20 3234767 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 1|0:1,0:48:1:51,51 1|0:1,0:48:8:51,51 0/1:0,1:43:5:.,. 0/1:0,1:35:4:. 0/0:0,0:17:2:. 1/1:1,1:40:3:.
20 4234567 microsat1 GTC C 50 PASS NS=3;DP=9;AA=G GT:HDS:GQ:DP 0/1:0,1:35:4 0/1:0,1:17:2 1/1:1,1:40:3 0/1:0,1:35:4 1/1:1,1:17:2 0/0:0,0:40:3
20 4234667 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 1|0:1,0:48:1:51,51 1|0:1,0:48:8:51,51 ./1:.,1:43:5:.,. 0/1:0,1:35:4:. 0/1:0,1:17:2:. 1/1:1,1:40:3:.
20 4234767 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:HDS:GQ:DP:HQ 0|0:0,0:49:3:58,50 1|1:1,1:3:5:65,3 1/0:1,0:41:3:. 0/1:0,1:35:4:. 0/1:0,1:17:2:. 1/1:1,1:40:3:.
20 4234967 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 2/1:35:4 1/2:17:2 1/0:40:3
20 4235968 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 1|0:1,0:48:1:51,51 1|0:1,0:48:8:51,51 0/1:0,1:43:5:.,. 0/1:0,1:35:4:. 0/0:0,0:17:2:. 1/0:1,0:40:3:.
20 4236679 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:HDS:GQ:DP:HQ 1|0:1,0:48:1:51,51 1|0:1,0:48:8:51,51 1/0:1,0:43:5:.,. 0/1:0,1:35:4:. 0/1:0,1:17:2:. 0/1:0,1:40:3:.