HaplotypeCaller VCF for PON

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Steven Bentley

• February 22, 2021 23:05

Dear all,

Regarding the Panel of Normal for Mutect2, am I able to create this based on VCFs from HaplotypeCaller?

Essentially, we have VCFs but not the BAMs readily available, and we are looking to make a PON.

Kind regards
Steve

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  Genevieve Brandt (she/her)

  • February 23, 2021 18:03

  Hi Steve,

  This would not be a recommended method because Mutect2 is different than HaplotypeCaller in how it calls variants. You can read more here: https://gatk.broadinstitute.org/hc/en-us/articles/360035890491

  Here is our documentation regarding how to create a panel of normals: https://gatk.broadinstitute.org/hc/en-us/articles/360035531132

  Best,

  Genevieve

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  David Benjamin

  • March 02, 2021 05:00

  Steven Bentley Following up on Genevieve's answer it is not only not recommended, it would be counterproductive.  The purpose of the PON is to filter technical and mapping artifacts, whereas we use the germline resource argument to model germline variation.  In most cases you should use the PON and the AF-only gnomAD germline resource provided in our public google buckets.

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  Steven Bentley

  • March 02, 2021 05:28

  Thanks for the advice Genevieve and David. It is very much appreciated.

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