Cool stuff Ensembl VEP can do: one click BioMart

The web VEP tool gives you a lot of useful information about your variants, but you may want more details, for example about the genes your variants overlap: maybe you want to fetch their sequences, homologues or protein domains. With a single click, you can go straight to BioMart, using your list of genes or known variants as your filter.

Above your results table, you’ll find the ‘Download’ options which include two links to BioMart. Click on the ‘Genes’ link to go into the Gene Mart, where the list of genes you’ve found will be added as a filter. If you click on the ‘Variants’ link, you’ll go into the Variation Mart, with any known variants which match your input variants as the filter. You can then add further filters, if you wish, and select the attributes you want to see, as you usually would with BioMart.

BioMart is very flexible, but has a limited capacity, so please do not use this option with whole genome variant data. We recommend a maximum of around 500 variants in your initial VEP query for this kind of analysis.

Of course, BioMart can only provide information about previously known variants. It will extract the IDs from the ‘Existing variants’, column and get information about them; it cannot provide you with any further information about novel variants.