Dear GATK teams:
I am using GATK4 mutect2 with "PON" to call somatic variants in tumor-normal mode ,then I found some of the variants were disappeared in the raw VCF,some of the variants were targeted the label of "panel of normals" comparing with the same sample that didn't use "PON" .
a)What are the rules of targeting variants "panel of normal" or not ?
b)Why some variants in the raw VCF just be removed or added?
I have read a lot of material about "PON" ,but there is no detailed explanation on how a "PON" works in somatic calls. As far as I observed, I believe the targeting rules is not just present in the "PON" reference file.
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