Analysing SNP Consequences on Genes and Proteins with Ensembl's Variant Effect Predictor

Since the launch of the Variant Effect Predictor (VEP), it has become a popular tool in analysing SNPs and other genomic variants in both Ensembl and Ensembl Genomes.  The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts and protein sequence.  

We will demonstrate how to identify:

• genes and transcripts affected by the variants
• location of the variants (e.g. upstream of a transcript, in coding sequence, in non-coding RNA, in regulatory regions)
• consequence of your variants on the protein sequence (e.g. stop gained, missense, stop lost, frameshift)
• known variants that match yours
• SIFT (functional) predictions for missense variants included for chicken, cow, dog, human, mouse, pig, rat and zebrafish, and PolyPhen predictions for human 

A variety of input formats are accepted, including tab-delimited, VCF and pileup format as well as variant identifiers.  We will demonstrate how the VEP can be accessed through the web interface, REST server and Perl script. 

More information: http://www.ensembl.org/info/docs/tools/vep/index.html

Citation: McClaren et. al. 10.1093/bioinformatics/btq330