I would like to be able to compare many samples to each other at a time to find the frequency of somatic SNP appearance across multiple samples. Are there any plans to allow for MuTect2 to make multiple comparisons at a time?
Every cancer is unique, much like a snowflake! If you did such an analysis, I would think you would pick up germline variants and sequencing artifacts.
So no, there are no plans as you mention.
I am not using it for tumor/cancer analysis, but rather to pick up all of the variants between different samples taken from a single individual. But good to know, thanks for the reply!