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PoN causing missed somatic variant call with Mutect2

amfgcpamfgcp Member
edited July 2 in Ask the GATK team
Hi, I've been running Mutect2 for somatic variant calling and I decided to created a panel of normals (PoN) using "CreateSomaticPanelOfNormals". I followed the instructions for GATK as that is the version I've been using.

When going through the differences in the somatic variants called by Mutect2 with and without the PoN I noticed a case I was not expecting: using the PoN, Mutect2 did not call a previously called somatic variant because it was located in the same position as one of the germline variants caught by the PoN (present in 4 of the ~20 samples used in its creation). I tried re-running Mutect2 with the parameter "--genotypePonSites true" hoping that maybe for this case the variant would not be filtered but as expected by the parameter description it was.

I'll leave a screenshot of IGV where on the bottom track is the missed somatic variant and on the track above that is the germline variant (present in 3 other samples that were also used to create the PoN).

I have checked the release notes for newer GATK versions but I found none that seemed to address this case. Could I be missing something? Is the mentioned behaviour expected? If it is, is there a plan to change it in a future release?



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