The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
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