Using GenomicsDB with GATK

GenomicsDB is packaged into gatk4 and benefits qualitatively from a large user base.

GATK tools such as GenomicsDBImport, SelectVariants and GenotypeGVCFs interact with GenomicsDB workspaces. Refer to the tool index for more information on how to use these tools.

The GenomicsDB CLI tools can be used to modify or query workspaces created using GATK tools.