摘要
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.
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.
基金
an Australian Postgraduate Award(University of New South Wales)to EI,Chain Reaction(The Ultimate Corporate Bike Challenge),the Office of Health and Medical Research,NSW Government,Australia
the National Health and Medical Research Council Principal Research Fellowship(Grant No.1135886)to SLD,NSW Government,Australia
the National Heart Foundation of Australia Future Leader Fellowship(Grant No.101204)to EG.
