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@SkyWarrior, I don't understand why using MakeSitesOnlyVcf before VariantRecalibrator would not be a good idea. Removing all samples and genotypes is not a problem since here the purpose is to filter variants on the whole cohort, correct?
Hi @bhanuGandham Thanks! It's currently running but I wasn't sure this was the best way to speed up the process. Since it is recommended to use "manageable" intervals for GenomicsDBImport with WGS (i.e. smaller than a whole chromosome)…
Hi @Geraldine_VdAuwera , Thank you very much for your help. Indeed, after using a --target_titv of 3.2, the FP proportion increases significantly. May I ask you, if the number of novel variants displayed on the tranche plot looks odd to you? It is…