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about germline resource.
Dear GATK Team,
I've been experimenting with calling somatic variants in tumor only targeted seq data using GATK4 mutect2. (I'll call this output is raw vcf)
And I run FilterMutectCalls for adding result(ex. PASS, germline risk ..). (I'll call this output file is filter vcf)
I have some questions.
- I'm bit confused when the gnomAD file works.
When make raw mutect2 vcf, gnomAD database is used?
Or when run FilterMutectCalls, gnomAD databse is used?
2.I think "germline risk" filter in filter vcf is only marked when variants exist in gnomAD database. Is it okay?