What is the best discordant pair structural variant caller at the moment?
The most popular one used to be BreakDancer. But that is lacking VCF output I think and is based on my knowledge from a couple of months ago.
I think some new discordant pair callers have been released the last couple of months but I didn't check them out yet.
Is BreakDancer still the go to discordant pair SV caller or are there other good / better options for discordant pair SV calling? A caller with a nice VCF output is preferred to make downstream processing easier.