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annotate test-data/vcfcommonsamples-test1-input2.vcf @ 3:0012529b72a3 draft default tip

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author anton
date Mon, 15 Sep 2014 14:50:31 -0400
parents 6a1a90ea160f
children
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1 ##fileformat=VCFv4.0
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2 ##fileDate=20090805
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3 ##source=myImputationProgramV3.1
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4 ##reference=1000GenomesPilot-NCBI36
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5 ##phasing=partial
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6 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
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7 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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8 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
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9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
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10 ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
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11 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
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12 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
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13 ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
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14 ##FILTER=<ID=q10,Description="Quality below 10">
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15 ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
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16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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17 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
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18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
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19 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
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20 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
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21 ##ALT=<ID=CNV,Description="Copy number variable region">
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22 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00003
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23 19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0/1:3,3
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24 19 112 . A G 10 . . GT:HQ 0|0:10,10 0/1:3,3
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25 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 1/1:43:5:.,.
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26 20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0/0:41:3:.,.
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27 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2/2:35:4:.,.
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28 20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0/0:61:2:.,.
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29 20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 1/1:40:3
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30 20 1235237 . T . 0 . . GT 0/0 .
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31 X 10 rsTest AC A,ATG 10 PASS . GT 0 0|2