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Michelle •
Pooling normal data in Mutect2
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?
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Michelle •
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See this tutorial, under the heading "A step-by-step guide to the new Mutect2 Panel of Normals Workflow".
In brief you need to:
- Run Mutect2 in single sample mode for each normal sample
- Use GenomicsDBImport on the VCF output from step 1 do create a GenomicsDB
- Run CreateSomaticPanelOfNormals on the GenomicsDB created in step 2
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David Parry •
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