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comparison test-data/vcffixup-test1.vcf @ 0:a03f346b6aae draft

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author devteam
date Thu, 19 Mar 2015 14:30:34 -0400
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children 9d7e64e4b9fc
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-1:000000000000 0:a03f346b6aae
1 ##fileformat=VCFv4.0
2 ##fileDate=20090805
3 ##source=myImputationProgramV3.1
4 ##reference=1000GenomesPilot-NCBI36
5 ##phasing=partial
6 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
7 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
8 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
9 ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
10 ##FILTER=<ID=q10,Description="Quality below 10">
11 ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
12 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
13 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
14 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
15 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
16 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
17 ##ALT=<ID=CNV,Description="Copy number variable region">
18 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
19 ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
20 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
21 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
22 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
23 19 111 . A C 9.6 . AC=1;AF=0.166667;AN=6;NS=3 GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
24 19 112 . A G 10 . AC=1;AF=0.166667;AN=6;NS=3 GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
25 20 14370 rs6054257 G A 29 PASS AC=3;AF=0.5;AN=6;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:.,.
26 20 17330 . T A 3 q10 AC=1;AF=0.166667;AN=6;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,.
27 20 1110696 rs6040355 A G,T 67 PASS AA=T;AC=2,4;AF=0.333333,0.666667;AN=6;DP=10;NS=3;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
28 20 1230237 . T . 47 PASS AA=T;AC=0;AF=0;AN=6;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,.
29 20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AF=0.5,0.166667;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3
30 20 1235237 . T . 0 . AC=0;AF=0;AN=4;NS=2 GT 0/0 0|0 .
31 X 10 rsTest AC A,ATG 10 PASS AC=1,1;AF=0.2,0.2;AN=5;NS=3 GT 0 0/1 0|2