It has been quite a while since we’ve blogged about the VEP (Variant Effect Predictor), and in that time we’ve added a whole load of new features, particularly to the downloadable script version.
Structural variants
The VEP now supports finding the consequences of structural variants, with input either in VCF or tab-delimited format. Using the web interface to the VEP you can visualise which transcripts and features your structural variants overlap by clicking through to the Region in Detail view:
The cache
We’ve really pushed the VEP script’s capabilities when using local “caches” (as opposed to using remote databases). Almost every feature of the VEP is now available when using the cache in offline mode. You can use a local FASTA file to quickly retrieve the sequences required to construct HGVS notations. You can even construct your own cache from a GTF file if your species isn’t supported by Ensembl.
Our cache for human now contains allele frequency data from phase 1 of the 1000 Genomes Project, and you can use these frequencies to filter your input (for example, you might want to filter out variants that are common in the combined European (EUR) population). We also now provide SIFT predictions for 8 species – human, mouse, zebrafish, pig, cow, chicken, rat and dog.
Plugins
We’re always trying to add new and useful features to the VEP, but we also recognise that other users have great ideas that they’d like to implement. The VEP script enables the use of plugins; these are bits of code that add extra functionality to the VEP. They can be used to retrieve data from remote sources, run external tools, filter output; pretty much anything you can think of can be accomplished in a plugin!
It’s easy to get started, and a basic plugin can be just a few lines of code – have a look at some of the examples we’ve created.
I recently added a plugin to retrieve data from dbNSFP – this is a great resource created by Liu et al in Houston, TX. They have, for every possible missense substitution in the human genome, pre-calculated pathogenicity scores, frequencies, conservation scores and a plethora of other things, and made all of this available as an easily downloadable file. To use this with the VEP, you just download the file and the plugin, run a couple of commands to get the data into the right format, and away you go – the VEP can now provide you with scores from LRT, MutationAssessor, MutationTaster, FATHMM and more for any missense substitution in your input.
Summary and HTML output
We had a number of requests for the VEP to provide summary statistics at the end of each run, and who are we to disappoint our loyal users?!? The VEP now writes a pretty HTML summary:
You can also view your output as HTML using the –html flag, which allows you to sort, filter and analyse your output on the fly.
Don’t hesitate to get in touch with us about the VEP – our developer mailing list is the best place for technical questions, with helpdesk for everything else.