| Table of Contents | ||||||||
|---|---|---|---|---|---|---|---|---|
|
Overview
Ensembl Variant Effect Predictor (VEP) is a powerful toolset for the analysis, annotation, and prioritization of genomic variants, including in non-coding regions. The VEP accurately predicts the effects of sequence variants on transcripts, protein products, regulatory regions, and binding motifs by leveraging the high quality, broad scope, and integrated nature of the Ensembl databases. In addition, it enables comparison with a large collection of existing publicly available variation data within Ensembl to provide insights into the population and ancestral genetics, phenotypes and disease.
...
Genes and Transcripts affected by the variants
Location of the variants (e.g. upstream of a transcript, in the 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, and associated minor allele frequencies from the 1000 Genomes Project
SIFT and PolyPhen-2 scores for changes to protein sequence
Using
Use the module name ensembl-vep to discover versions available and to load the application.
...
ARCC has tried testing the halpo (also see here) command, and although the command runs, we’re unable to actually generate any results due to not having a suitable data set. It does appear that a specific data set is required “input data must be a VCF containing phased genotype data for at least one individual and file must be sorted by chromosome and genomic position; no other formats are currently supported.”
Multicore:
The vep command can run across multicores, view the vep command for more details about the --fork option.
...