To better understand how your variants might be linked to disease, you can add information from DisGeNET to your VEP analysis. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature, to provide disease associations with genes and variants.
You can add DisGeNET to your VEP query in the online tool, the REST API endpoints and as a plugin to the command line tool. These will report back any diseases associated with the variants, the Pubmed ids of the papers these were reported in and DisGeNET scores for the variant/disease associations.
With the online tool and REST API endpoints, you will always receive just these three datapoints, however if you’re working on the command line, you can choose which datapoints to see, and also filter by the score or source.
In our coming release (Ensembl 104), DisGeNET results will be returned by our REST API in a new key-value pair format for easier parsing.