Pooling normal data in Mutect2

Question

[Michelle]

I need to pool a bunch of normal samples into a file called "pon" in mutect2 so I can run a chunk of code next. Does anyone know if there's a method to pool normal data into one file on mutect2?

Answer 1

[David Parry]

See this tutorial, under the heading "A step-by-step guide to the new Mutect2 Panel of Normals Workflow".

In brief you need to:

1. Run Mutect2 in single sample mode for each normal sample
2. Use GenomicsDBImport on the VCF output from step 1 do create a GenomicsDB
3. Run CreateSomaticPanelOfNormals on the GenomicsDB created in step 2

[Michelle]

Thank you!