VEST (Variant Effect Scoring Tool)
is a machine
learning method that predicts the functional significance of
missense mutations based on the probability that they are pathogenic.
The latest downloadable release is VEST 3.0. Dependency: SNVBox 3.0. last updated on 05/01/2014.
Our software is intended for those with substantial bioinformatics and
Linux system expertise and access to
VEST3 scores (for all non-silent variants) can be retrieved
automatically with the CRAVAT4.3 server.
Scores from the most recent version VEST4 can be retrieved
automatically with the CRAVAT5.0 server
VEST is free for non-commercial use. For more details please refer to our Software License. Commercial users should contact the Johns Hopkins Technology Transfer office
Documentation for the user
- This section provides documentation for the user, including instructions to download and install the source code.
Documentation for the developer
- This section provides documentation for developers.
- Short tutorial on how to run VEST from the command line
- Example running VEST on real data
- (L) Comparison with PPH2 and SIFT on gene holdout
- (R) Utility in network-based stratification of tumors
- If you use our software for a publication, please cite the following:
Carter H, Douville C, Yeo G, Stenson PD, Cooper DN, Karchin R (2013)
Identifying Mendelian disease genes with the Variant Effect Scoring Tool BMC Genomics. 14(3) 1-16.
Douville C, Masica DL, Stenson PD, Cooper DN, Gygax D, Kim R, Ryan M, Karchin R (2016)
Assessing the pathogenicity of
insertion and deletion variants with the Variant Effect Scoring Tool
(VEST-indel) Human Mutation 37(1):28-35.
Software primary contact/developer
Hannah Carter hcarte10 at gmail dot com
For issues with VEST run on the web with CRAVAT, please contact Rick Kim rkim at insilico dot us dot com