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 ?