Hi everybody!
I've just started working with all these bioinformatic analysis tools, so please forgive me if my question is stupid.
I am comparing the VCF files I get from SAMTools with the old Pileup files, and there is some information that is present in the Pileup but absent from the VCFs.
Highlighted below:
Pileup:
chr10 93489 G S 26 26 33 8 c,,,cc,, W]Z]QMZJ
VCF:
chr10 94083 . C T 71 . DP=43;AF1=0.5;CI95=0.5,0.5;DP4=5,5,2,25;MQ=23;FQ=47;PV4=0.0092,4.4e-22,1,1 GT:PL:GQ 0/1:101,0,74:77
Does anyone know how to extract this info using the VCF format?
Thanks a lot
Amit
I've just started working with all these bioinformatic analysis tools, so please forgive me if my question is stupid.
I am comparing the VCF files I get from SAMTools with the old Pileup files, and there is some information that is present in the Pileup but absent from the VCFs.
Highlighted below:
Pileup:
chr10 93489 G S 26 26 33 8 c,,,cc,, W]Z]QMZJ
VCF:
chr10 94083 . C T 71 . DP=43;AF1=0.5;CI95=0.5,0.5;DP4=5,5,2,25;MQ=23;FQ=47;PV4=0.0092,4.4e-22,1,1 GT:PL:GQ 0/1:101,0,74:77
Does anyone know how to extract this info using the VCF format?
Thanks a lot
Amit
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