VPOT:A Customizable Variant Prioritization Ordering Tool for Annotated Variants

作     者：Eddie Ip Gavin Chapman David Winlaw Sally LDunwoodie Eleni Giannoulatou 

作者机构：Victor Chang Cardiac Research InstituteSydney 2010Australia St Vincent’s Clinical SchoolUniversity of New South WalesSydney 2052Australia Heart Centre for ChildrenThe Children’s Hospital at WestmeadSydney 2145Australia Sydney Medical SchoolUniversity of SydneySydney 2050Australia School of Biotechnology and Biomolecular SciencesUniversity of New South WalesSydney 2033Australia 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2019年第17卷第5期

页      面：540-545页

核心收录：

学科分类：0710[理学-生物学] 0831[工学-生物医学工程（可授工学、理学、医学学位）] 0711[理学-系统科学] 1001[医学-基础医学(可授医学、理学学位)] 07[理学] 08[工学] 0714[理学-统计学（可授理学、经济学学位）] 0703[理学-化学] 0701[理学-数学] 0812[工学-计算机科学与技术（可授工学、理学学位）] 

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 

主　　题：Next-generation sequencing Pathogenicity predictions Variant prioritization Customizable ranking Genomic annotation 

摘      要：Next-generation sequencing(NGS) technologies generate thousands to millions of genetic variants per *** of potential disease-causal variants is labor intensive as it relies on filtering using various annotation metrics and consideration of multiple pathogenicity prediction *** 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 *** use of VPOT can be informative when analyzing entire cohorts,as variants in a cohort can be *** also provides additional functions to allow variant filtering based on a candidate gene list or by affected status in a family *** outperforms similar tools in terms of efficacy,flexibility,scalability,and computational *** is freely available for public use at Git Hub(https://***/VCCRI/VPOT/).Documentation for installation along with a user tutorial,a default parameter file,and test data are provided.