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How to include non variant sites in the output vcf of GenotypeGVCFs?

SamwittwerSamwittwer Zurich, SwitzerlandMember


I'd like to include confident non variant sites in my downstream analyses. If I understand correctly, this was possible in previous versions with --includeNonVariantSites but I'm not seeing an option that allows me to do this in GATK4. Am I missing something obvious or is this currently not possible?

Thank you very much in advance and best wishes


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