The VCI should not generate an ERepo link for non-EP groups

[cgpreston]

Reported for a non-ClinGen affiliation in the VCI:

The current ClinVar submission process generates an ERepo link if groups are using the ClinVar submission, the link is not active but ideally we would not generate the link at all.

Please first investigate and report back on the effort required to address this ask.

[bryanwulf]

Example of problem:
Variant: 143533
Affiliation: Centre for Population Genomics
ClinVar URL (with link to ERepo): https://www.ncbi.nlm.nih.gov/clinvar/variation/143533/

To prevent these links from appearing in the future, I think most (if not all) of the effort will fall to those maintaining the ClinVar submitter service (Larry's team). If the existing links need to be removed, we're probably looking at multiple days of effort to find the affected variants and generate new submission files (for respective affiliations to submit to ClinVar).

[cgpreston]

@bryanwulf thanks, what would be the estimate of effort to no longer generate these links going forward?

[bryanwulf]

If we need to make changes (say, to the data that the VCI sends to the ClinVar submitter service), I don't think they would require a lot of time (on a scale of days).

[cgpreston]

Feedback on 11/18: VC proxies said that the goal would be to stop generating the links, not to retrospectively remove the one's already generated. It sounds like the next step would be to synch with the submission service team.