Mutect2 tumor-only mode without normal match or germline resources
Hi, If I use Mutect2 in tumor-only mode to call somatic variants without any normal match, panel of normals (PON) or other germline resources. Will the results contain many germline variants? Will the results be very similar to using HaplotypeCaller? Thank you!
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Hi Leo
Short answer: No.
Mutect2 uses a different model compared to HaplotypeCaller when calling variants and not using any PoN, germline resource or a matched normal will make Mutect2 to push more false positive calls to PASS filters after FilterMutectCalls step. Mutect2 is more naive and will almost call any different looking site as a variant as opposed to HaplotypeCaller which uses a germline model as a prior for calling variants.
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