Calculate Simple Somatic Mutations from sliced BAM

Question

[michal.devir]

Hi,

I would like to retrieve simple somatic mutations (using mutect2) from a bam file. However, I am interested in mutations in specific areas in the DNA only (for example, specific chromosoms). Can I calculate the mutations based on a sliced bam file? or should I first run the tool to generate the somatic mutations file, and then slice it?

Thanks, Michal.