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Test-drive the GATK tools and Best Practices pipelines on Terra
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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 (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/) 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?