Ip, Eddie and Chapman, Gavin and Winlaw, David and Dunwoodie, Sally L. and Giannoulatou, Eleni (2019) VPOT: A Customizable Variant Prioritization Ordering Tool for Annotated Variants. Genomics, Proteomics & Bioinformatics. ISSN 16720229
Full text not available from this repository.Abstract
Next-generation sequencing (NGS) technologies generate thousands to millions of genetic variants per sample. Identification of potential disease-causal variants is labor intensive as it relies on filtering using various annotation metrics and consideration of multiple pathogenicity prediction scores. We have developed VPOT (variant prioritization ordering tool), a python-based command line tool that allows researchers to create a single fully customizable pathogenicity ranking score from any number of annotation values, each with a user-defined weighting. The use of VPOT can be informative when analyzing entire cohorts, as variants in a cohort can be prioritized. VPOT also provides additional functions to allow variant filtering based on a candidate gene list or by affected status in a family pedigree. VPOT outperforms similar tools in terms of efficacy, flexibility, scalability, and computational performance. VPOT is freely available for public use at GitHub (https://github.com/VCCRI/VPOT/). Documentation for installation along with a user tutorial, a default parameter file, and test data are provided.
| Item Type: | Article |
|---|---|
| Subjects: | R Medicine > R Medicine (General) |
| Depositing User: | Repository Administrator |
| Date Deposited: | 09 Dec 2019 03:03 |
| Last Modified: | 09 Dec 2019 03:03 |
| URI: | https://eprints.victorchang.edu.au/id/eprint/901 |
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