I am using GATK 18.104.22.168. This version includes the new FilterMutectCalls module.
I was wondering, is there anything different that Mutect2 does in tumor-only mode vs. in matched-normal mode? In theory, every mutation in the matched-normal should be in the tumor-only mode, correct?
If there is any difference, I suspect it would be in the FilterMutectCalls portion, if I am not mistaken. There seems to be a germline filter that I'm not sure how would work. For example, I see in the documentation this given as an example command:
gatk Mutect2 -R ref.fasta -I tumor.bam -O unfiltered.vcf
I'm not sure how some of Mutect's filters like the germline filter would work in this case. Does Mutect2 just ignore this filter?
Please sign in to leave a comment.