Were you planning on attending or hosting an Ensembl workshop in 2020, but your plans got cancelled due to the SARS-CoV-2 pandemic? All is not lost, as we’re still providing live virtual training and here’s how it works.
Continue readingTag: REST API
Normalising variants to standardise Ensembl VEP output
Variants can be represented in myriad different ways; indeed, Ensembl VEP currently supports input in many different formats, including VCF, HGVS and SPDI. However, even within these specifications, variants can be described ambiguously. Insertions and deletions within repeated regions can be described at multiple different locations. For example, VCF describes variants using their most 5’ representation, while HGVS format describes a variant at its most 3’ location.
Starting in Ensembl 100, VEP optionally normalises variants within repeated regions by shifting them as far as possible in the 3’ direction before consequence calculation. This standardises VEP output for equivalent variant alleles which are described using different conventions.
Ensembl is part of the first Google Season of Docs!
Google Season of Docs (GSoD) provides a framework for technical writers and open source projects to work together remotely towards the common goal of improving an open source project’s documentation. This exciting new programme ran for the first time from September to November 2019!Continue reading
A guide to hosting an Ensembl Workshop
Are you interested in having us come to your institute to deliver an Ensembl workshop, but are not quite sure what it involves? This blog is a guide for you.
Ensembl 96 and Ensembl Genomes 43 are out!
These releases are huge in many respects, so it was difficult to decide which news to put first! Let’s start with some exciting news from our annotators.Continue reading
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.
More Ensembl training options available
You might know that we offer training courses on using the Ensembl browser, but did you know that we also offer Ensembl REST API and Ensembl Train the Trainer courses? We can come to you to deliver any of these courses at your institute and we don’t charge any fees. If you’re in a low-middle income country, we don’t even charge you for expenses.
The new Ensembl regulatory build for mouse
You may have heard us squeaking about our new mouse regulatory build in our Ensembl 93 release blog. If you’re interested in finding out what exactly a ‘regulatory build’ is, and how to view and download this data in Ensembl, then this is the blog for you!