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.

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @prosium
    Hi,

    Yes, the PoN is important in catching artifacts as well as possible germline events that are missed in the matched normal and germline resource. Have a look at this document.

    -Sheila

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    I agree with @Sheila, and want to add that due to improvements in GATK 4 Mutect2 the PoN is gradually becoming less important. It is very important in GATK3 and slightly useful to sort of important (depending on read/fragment lengths and other things that influence mapping quality) in GATK4.

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