Cool stuff the Ensembl VEP can do: take a REST

The VEP can work as an offline or a web tool and it’s also available as REST service. Perfect for integrating into pipelines or displaying data on the web, the REST API VEP endpoints can take input as HGVS, genomic loci or variant identifiers and can interpret common forms of non-standard HGVS. They are all available using both GET and POST protocols, supporting queries on single or multiple variants respectively.

Just like when using the offline tool, you can use the VEP plugins with REST, adding them as optional parameters in the REST query. For example, you can get dbNSFP LRT and MutationTaster predictions by adding the options:

dbNSFP=LRT_pred,MutationTaster_pred

The output is available as JSON, JSONP and XML, making it easy to decode in your chosen programming language, and pick out the data you need. We have an online course on using REST APIs, including instruction on calling REST API endpoints, decoding JSON outputs and using both GET and POST endpoints.

Run VEP endpoints with the REST API to get quick plain-text data. It will even work with non-standard HGVS, as shown here.

There is a limit of 200 variants on the POST requests and the whole REST API is rate-limited at 55000 requests per hour, so running the offline tool is still the best method for large-scale analysis.

Leave a Reply

Your email address will not be published. Required fields are marked *