How to interpret the output of gatk?

Question

[Laven9]

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.

Answer 1

[zephyr_falcon]

It seems like you ran tumor-only mode of Mutect2. Did you only put tumor bam file as an input?

Mutect2 needs 2 bam files for accurate mutation calling: tumor and its matching normal.

If you just use a tumor bam file, it will also call false positives which may lead to larger number of somatic mutations.

You could refer https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php

for the other command options.