Currently, the "include ref calls" option is on by default in the upload dialog. That should not always be the case, as when processing 1000g VCFs, as it would take forever to process the extra, unnescessary, reference genomes. However, this checkbox is expected to be consistent per project.
[x] Add the checkbox to the project wizard
[x] Save the setting to the project
[x] Use the setting instead of the checkbox in the Upload App
[x] If editing this setting on an existing project, show a warning that current imported VCFs would need to be re-uploaded to access their reference calls.
Currently, the "include ref calls" option is on by default in the upload dialog. That should not always be the case, as when processing 1000g VCFs, as it would take forever to process the extra, unnescessary, reference genomes. However, this checkbox is expected to be consistent per project.