How to interpret the output of gatk?
Entering edit mode
2.5 years ago
Laven9 • 0

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.

gatk mutect2 vcf2maf • 1.0k views
Entering edit mode
2.5 years ago

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

for the other command options.


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