Recently I run Gatk-Mutect2 to call the somatic mutations in my data, but I get a lot more (too much and seems abnormal) mutations than I expected. I supposed that there should be some filter I need to do to filter out those germline mutations. But I am not quite sure what filters should I do. Is there a column that contains information of germline or somatic? Or is there any steps I should run?
I only run Mutect2 (input:bam) to get my result.