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comparison test-data/vcfallelicprimitives-test1.vcf @ 0:3f4fefbc52c8 draft

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author devteam
date Thu, 19 Mar 2015 12:23:24 -0400
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-1:000000000000 0:3f4fefbc52c8
1 ##fileformat=VCFv4.0
2 ##fileDate=20090805
3 ##source=myImputationProgramV3.1
4 ##reference=1000GenomesPilot-NCBI36
5 ##phasing=partial
6 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
7 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
8 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
10 ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
11 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
12 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
13 ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
14 ##FILTER=<ID=q10,Description="Quality below 10">
15 ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
17 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
19 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
20 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
21 ##ALT=<ID=CNV,Description="Copy number variable region">
22 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
23 ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
24 ##INFO=<ID=Split primitives,Number=0,Type=Flag,Description="The allele was parsed using vcfallelicprimitives.">
25 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
26 19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
27 19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3
28 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:.,.
29 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:.,.
30 20 1110696 . A G,T 67 PASS AF=0.333,0.667;LEN=1,1;TYPE=snp,snp;Split primitives GT 1|2 2|1 2|2
31 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:.,.
32 20 1234567 . G GA,GAC 50 PASS AC=3,1;LEN=1,2;TYPE=ins,ins;Split primitives GT 0|1 0|2 1|1
33 20 1235237 . T . 0 . . GT 0/0 0|0 .
34 X 10 . AC ATC,A 10 PASS LEN=1,1;TYPE=ins,del;Split primitives GT 0 0|2 0|1
35 X 11 . C G 10 PASS LEN=1;TYPE=snp;Split primitives GT 0 0|0 0|1