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SelectVariants and discordance
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?