Is this the good way to parse var.vcf files ?

Hi everyone,

I have to parse var.vcf files for my work and I'm wondering if I'm doing this correctly. For example with this line :

Chr1    204346    .    G    A,C    138    .    DP=360;VDB=0.0143;AF1=1;AC1=2;DP4=1,1,208,126;MQ=35;FQ=-282;PV4=1,0.01,0.48,1    PL    171,255,0,172,35,25

First I check for all bases possibilites : GG, GA, AA, GC, CA, CC

After that I look at the PL field and choose the bases with the index of the lowest value in this field.

So in my case it will be AA.

Is this correct ?

snp

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updated 10.9 years ago by vassialk •

• written 10.9 years ago by jsgounot

Ummm, what are var.vcf files? Are they a special type of VCF files?

• 0 views • link

written 10.9 years ago by Ram

0 answers

No answers yet.

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