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Does setting the -out_mode flag in UnifiedGenotyper differently has different effect when doing VQSR
Does VQSR behave differently when the
-out_mode flag in UnifiedGenotyper is set to
EMIT_VARIANTS_ONLY as compared to
EMIT_ALL_CONFIDENT_SITES. I think by using
EMIT_ALL_CONFIDENT_SITES we might give VQSR more information to train the model, but I may be wrong. Can someone please help me with this ? Thanks.