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Filtering Mutect2 somatic calls with PoN dataset


I have build my PoN data and would like to filter out artifacts and germ-line variants by inspecting a panel of normal samples and rejecting candidates that are present >= 2 normal samples. [According to methods in Cibulskis et al. Nat Biotechnol 2013]

My query is that some of my somatic point mutations overlap with germline indel calls or somatic indels overlap with germline SNPs. In these cases, should I filter out the somatic calls as stated above?

Thanks for your input!

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