Pooling normal data in Mutect2
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5 weeks ago
Michelle • 0

So here's the sample files I have here.

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?

mutect2 pooling normal samples panelofnormals • 268 views
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4 weeks ago
David Parry ▴ 80

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
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Thank you!

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