Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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.


  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    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.


  • 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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