Hi, I ran mutect2 with the default setting. And I got all of the mutations marked "alt_allele_in_normal". I just want to know if this is OK? Should it be some of the mutations marked alt_allele_in_tumor?
this means that all variants which are found in your tumor sample are found in your matched normal too. Tumor specific/eclusive variants would have a "Pass" in the filter field if they dont get hit by some of the other filters of mutect2.