Create Somatic PON threshold

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Pedro Miguel Raposo

• July 31, 2020 14:53

Hello GATK Team,

I have a simple question when it comes to creating a somatic PON. Under the 'CreateSomaticPanelOfNormals' description it says that "The tool takes multiple normal sample callsets produced by Mutect2's tumor-only mode and collates sites present in two or more samples into a sites-only VCF". Does this means that a variant present in at least 2 of the total samples used, is going to be introduced into the PON? If so, the more samples used, the more likely variants are going to be common between samples. With this, should there be a reasonable maximum number of samples used to create a PON, so that we don't have false positives in the PON?

Thank you,

Pedro Raposo

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  Genevieve Brandt (she/her)

  • August 03, 2020 21:51

  Hi Pedro Miguel Raposo:

  Please see this for more information about the Mutect2 algorithm:

  • https://www.biorxiv.org/content/10.1101/861054v1

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

  Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

  We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

  For context, check out our support policy.

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