CombineVariants + filtering

lindenblindenb FranceMember ✭✭

Hi GATK team,

I've been asked to merge a large number of VCF file (one sample/vcf) but only if QUAL is lower than a given value. I would like to avoid to filter+copy each VCF and then merge with CombineVariants.
So my question is: is it possible to give a (JEXL?) expression to accept/reject a variant in one vcf ?

Thanks !

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