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Old 04-03-2013, 07:35 PM   #3
Location: US

Join Date: Dec 2012
Posts: 16

Thanks swbarnes2

Could you explain a little more why "use samtools mpileup on both .bams together" will work? In that case, we still need the reference genome from subspecies A, right?

Another thing is that: if there are more than 1 non-reference allels reported, the samtools only gives out the depth of the 1st non-reference allel (as listed in DP4). Also, although the 1/1 indicates homozygous alternate, I don't understand the meaning of the PL value which is "131,59,26,91,0,85" (as shown below). How can we get the depths and other information for the 2nd alternate ?

chr2 213263 . A C,T 72 . DP=14;VDB=0.0355;AF1=1;AC1=2;DP4=0,0,9,4;MQ=56;FQ=-60 GT:PL:GQ 1/1:131,59,26,91,0,85:63
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