I think this should be an easy one so I apologize if it's a stupid question.
I'm confused from reading the Best practices workflow for Germline short variant discovery.
I am trying to get a set of "analysis-ready variants".
I've run ApplyVQSR on my VCF file. What step comes next? Am I suppose to now run CNNScoreVariants on my VCF file? Or do I run FilterVariantTranches?
I can't tell if that is now the assumed best practice or if I should just run CNNScoreVariants only.
Thanks in advance for any and all help.
Please sign in to leave a comment.