SelectVariants and discordance
Posted in Ask the GATK team | Last updated on


Comments (3)

Greetings GATK team!

I hope I'm not making a duplicate question here, but I couldn't find anything regarding this in the forum.

Basically, what I want to do is to use SelectVariants to filter against another call set, but I do not want to be as strict as using -discordance (i.e. 100% discordance rate between the two call sets). I want to say for example: "filter call set A against variants that occur in >90% of call set B".

Is there a way to do this with JEXL expressions maybe?

Kind regards


Return to top Comment on this article in the forum