Attention: Want an end-to-end pipelining solution for GATK Best Practices?
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