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Old 12-05-2010, 11:43 AM   #1
Location: Massachusetts

Join Date: Feb 2009
Posts: 50
Default How to understand the output of mpileup like this

vcf was generated by samtools-0.1.12
In the following line of output:

1 8075 . A C 99 . DP=7;AF1=0.9999;CI95=0.5,1;DP4=0,0,2,5;MQ=37 PL:GT:GQ 0,0,0:1/1:39 143,21,0:1/1:60

It tells me that the genotype likelihoods of sample1 are P(D|AA)=1, P(D|AC)=1, P(D|CC)=1?
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