This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
How to include non variant sites in the output vcf of GenotypeGVCFs?
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