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reason for using -new-qual in GenotypeGVCFs
I am aware that -new-qual switch in GenotypeGVCFs uses a new algorithm to calculate AFs. Can I get more details of it with examples on why should it be used instead of the old one (about which also I would like to know)? On quick look, I saw that the variant quality (QUAL) was different for a particular variant site with and without the usage of -new-qual.