We had a number of queries about the Ensembl VEP related to its support for SARS-CoV-2. Here, we talk about how you can use the command line VEP to analyse your variants against the SARS-CoV-2 gene set from Ensembl.Continue reading
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.
The Ensembl VEP does not only allow you to annotate short variants, such as SNPs and short insertions or deletions, but also some types of structural variants.