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Old 12-02-2012, 12:49 AM   #1
tahamasoodi
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Default samtools output

How can i locate the genotype from the vcf file of samtools? Here are two variants with their info. What does 0/1 and 1/1 signify?

INDEL;DP=22;AF1=0.5032;CI95=0.5,0.5;DP4=1,0,4,0;MQ=26;FQ=-15.7;PV4=1,1,0.17,0.4 GT:PLP:GQ 0/1:48,0,19:5:22

DP=11;AF1=1;CI95=0.5,1;DP4=1,0,0,9;MQ=15;FQ=-34;PV4=0.1,7.7e-06,0.046,0.33 GT:PLP:GQ 1/1:41,7,0:10:57
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Old 12-02-2012, 07:32 AM   #2
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There is no answer for the above question.
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Old 12-02-2012, 12:59 PM   #3
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You posted in the middle of Saturday night in America, and Sunday morning in Europe. What did you expect?

You didn't even post the whole line. 0/1 means the software thinks it's a heterozygous variant, 1/1 means the software thinks it's homozygous for the ALT variant.

But coverage is rather low on those loci, so those assessments are a little dubious.
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Old 12-02-2012, 10:00 PM   #4
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Where is the genotype and how did you say the coverage is low on these loci? See the whole lines:

chr1 10177 . A C 47 . DP=65;AF1=0.5;CI95=0.5,0.5;DP4=4,20,6,10;MQ=20;FQ=50;PV4=0.16,0.0022,1,1 GT:PLP:GQ 0/1:77,0,103:40:80
chr1 10230 . acccc accc 4.71 . INDEL;DP=63;AF1=0.8277;CI95=0.5,1;DP4=0,1,0,7;MQ=27;FQ=-33.5;PV4=1,0.1,0.0054,1 GT:PLP:GQ 1/1:39,0,1:8:5
chr1 10309 . C T 17.1 . DP=9;AF1=0.5;CI95=0.5,0.5;DP4=2,0,0,3;MQ=29;FQ=11.7;PV4=0.1,0.0055,1,1 GT:PLP:GQ 0/1:47,0,39:5:41
chr1 10315 . C T 63.3 . DP=8;AF1=1;CI95=0.5,1;DP4=0,0,2,3;MQ=29;FQ=-42 GT:PLP:GQ 1/1:96,15,0:5:75
chr1 10329 . acccc accc 4.91 . INDEL;DP=9;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=24;FQ=-40.5 GT:PLP:GQ 1/1:42,6,0:2:49
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Old 12-03-2012, 10:37 AM   #5
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Can anybody throw more light on this?
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Old 12-03-2012, 10:56 AM   #6
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VCF version 4.1
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