GWAVA

GWAVA

GWAVA

Overview

GWAVA is a tool which aims to predict the functional impact of non-coding genetic variants based on a wide range of annotations of non-coding elements (largely from ENCODE/GENCODE), along with genome-wide properties such as evolutionary conservation and GC-content.

To use GWAVA you can either download the software and necessary annotation files and run it locally, or you can access pre-computed scores and annotations from a webserver with annotations for all known variants (from Ensembl release 70). A plugin for the Ensembl Variant Effect Predictor is also available from the download page.

If you have any problems with or questions about this resource please contact Graham Ritchie.

Download and Installation

Learn and Support

GWAVA is a tool which aims to predict the functional impact of non-coding genetic variants based on a wide range of annotations of non-coding elements (largely from ENCODE/GENCODE), along with genome-wide properties such as evolutionary conservation and GC-content.

The web server provides pre-computed annotations and GWAVA scores for all known variants from the Ensembl variation database (release 70, including over 50 million variants). To search the database, use the search box below to enter a list of variant identifiers (each on their own line) or a chromosomal region, specified in the form chr:start-end, which will retrieve results for all known variants in that region, for example chr1:1000000-1010000.

The results include the prediction scores from 3 different versions of the classifier, which are all in the range 0-1 with higher scores indicating variants predicted as more likely to be functional, and the underlying annotations used to compute these scores. For more details please refer to the GWAVA paper. If you want to retrieve scores for a large number of variants we recommend that you tick the checkbox below to export the results to a CSV spreadsheet rather than trying to display them in the browser. A complete set of pre-computed scores are available for download as a BED format file from the GWAVA FTP site

License and Citation

All source code written for GWAVA is released under the Apache License, Version 2.0.

If you make use of this software in your research please cite as follows :

Ritchie GR, Dunham I, Zeggini E and Flicek P, Functional annotation of noncoding sequence variants.

Contact

If you have any problems with or questions about this resource please contact Graham Ritchie.

Publications

  • Functional annotation of noncoding sequence variants.

    Ritchie GR, Dunham I, Zeggini E and Flicek P

    Nature methods 2014;11;3;294-6

Tool Type