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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.

Consensus PON for hg19 Mutect2

Hi GATK Team,

Is there a human consensus PON that is available for mutation calling in Mutect2? From my understanding both TCGA ( and Broad use a generalized PON.

If this is not available, what is the best practice for single pair (tumor/normal matched) calling in Mutect2? Is there a difference between generating a PON from the single normal or not using a PON and just passing the tumor and normal into Mutect2?



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