VPOT:A Customizable Variant Prioritization Ordering Tool for Annotated Variants |
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| Affiliation: | Victor Chang Cardiac Research Institute, Sydney 2010, Australia;St Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia;Heart Centre for Children, The Children's Hospital at Westmead, Sydney 2145, Australia;Sydney Medical School, University of Sydney, Sydney 2050, Australia;Victor Chang Cardiac Research Institute, Sydney 2010, Australia;St Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia;School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2033, Australia |
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| 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 Git Hub(https://github.com/VCCRI/VPOT/).Documentation for installation along with a user tutorial,a default parameter file,and test data are provided. |
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| Keywords: | Next-generation sequencing Pathogenicity predictions Variant prioritization Customizable ranking Genomic annotation |
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