MuTect2 and smalls mpileup reads info seem to be very different?
Hi - I used MuTect2 to call variants in multiple samples from one patient. However, I wanted read information for those samples where a mutation wasn't detected in all the samples and decided to use samtools mpileup at these sites. I noticed that a variant in a germline sample was reported as 24:0 ref:alt (MuTect2) and 104:25 (samtools). In one case, I'd call it a somatic mutation while it would be a gremlin mutation in the other case. Why do we see this difference? Is there a way to make MuTect2 output read info when it detects a mutation in one of the samples from a patient?