A project can be created with multiple references checked, but there doesn't seem to be any mechanism for selecting which reference a set of uploaded VCFs pertains to. In the admin section, when uploading a variant file, there is a notice in the import variants wizard:
This wizard will help you import variants for:
projectname (hg19)
If the variants are with respect to another reference genome, switch to that reference and try importing again
There are no instructions provided on how to switch to another reference, and it is likely not possible with the current UI.
Potential fixes:
Prompt user to select a single reference whenever they upload a set of VCFs.
A project can be created with multiple references checked, but there doesn't seem to be any mechanism for selecting which reference a set of uploaded VCFs pertains to. In the admin section, when uploading a variant file, there is a notice in the import variants wizard:
This wizard will help you import variants for: projectname (hg19) If the variants are with respect to another reference genome, switch to that reference and try importing again
There are no instructions provided on how to switch to another reference, and it is likely not possible with the current UI.
Potential fixes: