Should I make PON although having Matched normal samples? PLEASE LET ME KNOW (..)
I have normal-tumor matched samples for 30 individuals.
but Every documents i saw says 'Making PON is a very important process'.
Although i have matched normal samples with every tumor samples, should i make pon using Mutect tumor only mode?
ps. I currently use GATK3. And want to compare GATK3 and GATK4 in the view of result.