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Hi, I'm running UnifiedGenotyper with different glm values (BOTH, INDEL, SNP).
I expected that the set of variants from glm BOTH is the same as the union of variants from glm SNP and INDEL, but it wasn't.
Althought the different was not big (less than 100 variants), I'm curious why there's such a difference and want to know which is better way to find variants (both snps & indels).