VEP 94.5

Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Simply input the coordinates of your variants and the nucleotide changes to find out the:

  • 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, and associated minor allele frequencies from the 1000 Genomes Project
  • SIFT and PolyPhen scores for changes to protein sequence
  • ... And more!

Accessing the software

To load the module:

$ module load VEP/94.5-iomkl-2018a-Perl-5.26.0

To view a list of command-line options, run the following command:

$ vep

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions of this application are recorded below:

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Visit the VEP website for more information regarding this application.


Last modified: 18 January 2019