How does VariantEval's CountVariants option determine MNPs?
I am trying to understand what CountVariants is calling as an MNP in my dataset. When I run CountVariants, I get ~3K MNPs called across my samples. However, when I run SelectVariants with -selectType MNP (and -selectType MIXED), or when I run VariantAnnotator with -A VariantType, nothing seems to be identified as an MNP in my base VCF.
Is CountVariants running additional processes that I'm missing?