I am working on some human WGS tumor samples and I want to call somatic variants against the normal tissue sample. I see that Mutect2 had a tumor-mode in previous Mutect2 (now deprecated) guidelines but I can not find it anymore in current GATK Mutect2 guidelines where only PoN are used.
Does it mean that I cannot compare 2 samples directly anymore? Shall I just put the normal tissue in the PoN with other samples? What would be a good way to have a direct comparison between normal and tumor samples (maybe after applying a Panel-of-Normals filter too).
Thank you in advance for any help!