How does a panel of normal affect variant calling using mutect2
I am running an analyis on tumor samples using mutect2. To investigate the effect of a PON on variant calling , I ran my analysis with and without the PON. Both analyses yield different amounts of called variants, as expected more for the analysis without the PON. But there are still variants in the analysis with PON marked as filtered on basis of the PON.
That surprises me as I thought mutect would do the calling and then filter variants marked as being site-specific artefacts. However, based on the reduced number of variants called plus variants filtered PON-wise
I conclude that mutect affects variant calling in (at least) two different ways. I would appreciate if you can clarify this.