Hi Yuzhang,
I think you miscalculated the permutations.
Here VCF specs with the answer to your question:
http://samtools.github.io/hts-specs/VCFv4.3.pdf
Off the top of my head, answer is that PLs are (R is REF and A is ALT):
RR,RA1,RA2,RA3,A1A1,A1A2,A1A3,A2A3,A2A2,A3A3
I could be wrong about the order, but the answer is somewhere in the VCF specs.
Best wishes,
Tommy
From: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Date: Tuesday, 8 March 2016 02:16:00
To: samtools-help
<[email protected]<mailto:[email protected]>>
Cc: zgyu12 <[email protected]<mailto:[email protected]>>
Subject: [Samtools-help] samtools PL
Hi dear:
Thanks for your attention.I got some problems when using samtools.
The VCF file contain an entry:
Supercontig_1.1 104341 . G A,T,C 126 .
DP=9;VDB=0.0030;AF1=1;AC1=2;DP4=0,0,4,4;MQ=60;FQ=-45 GT:PL:DP:GQ
1/1:159,18,0,158,8,155,158,8,153,155:8:33
There are 3 ALTs and the PL contain 10 fields.I can not get the
meaning of the 10 fields.Should they be 9?How to unstand the DP4 in this case?
Thanks a lot ;
Best Regards,
yuzhang
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