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Create separate panels of normals for SNVs and Indels?

Hello,

I have created a panel of normal with >200 normal samples by running mutect2 in tumor-only mode followed by CreateSomaticPanelOfNormals.
I have come across a few examples where the normals in the PON have indels at a particular site, but the somatic VCF has a SNV called at the exact same position, which then gets filtered because of the PON.
Similarly, I have seen sites in the PON because of recurrent SNPs in the normals, but that leads to filtering of an indel from the somatic VCF. These somatic calls looked real when I looked at them in IGV.
I was thinking of creating separate PON from SNVs and indels called in the panel of normal, and doing a type-specific filtering of the somatic variants. I am hoping that that way sites where we find both SNPs and indels recurrently will be seen in both the lists, but a site where we only find SNPs recurrently will not make it to the indel PON and vice versa.
I wanted to know if this is something that you have already tried, and would you recommend it?

Answers

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