If you don’t want to analyse your variants on external servers or have more than 1000 or so to annotate, you probably want to use the VEP script. Setting it up might not always be straightforward as there are dependencies you need, but the installation script takes away a lot of the trouble.
Tag: variant effect predictor
Ensembl produce high quality gene annotation for a number of species, but getting it to the high quality we expect takes time. This means there are many species and strains where we don’t have annotation yet. If you’re working with a species without Ensembl annotation (like Trixie the Triceratops here) or even a specific strain that we don’t have, you can still make use of VEP for predicting the effect of variants on genes and transcripts, using your own annotation. All you need is a GFF or GTF of the transcripts, and a FASTA file of the genome.
Some Variant Effect Predictor (VEP) jobs are small, just ten or fewer variants, and that’s easy. Some VEP jobs are big, if you do variant calling on one whole human genome, that’s five million variants! The more variants you have, the more computing power the VEP needs to process them, which can make it slow. But there are ways to speed it up.