We shouldn't place a foreign key requirement for references when someone does not have them, or doesn't want to manage them. This means that a VCF should be able to be added with no other data (other than a dataset) present in a server.

The problem becomes that it is unclear what reference names to use to query a variant set. From the perspective of the server, that is a data management problem and the more full-fledged offering can be made by adding a reference set, but it shouldn't be required.