AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification.
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AutoGVP：集成了 ClinVar 和 InterVar 种系序列变异分类的 Docker 化工作流程。
DOI：
10.1101/2023.11.29.569103
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Diskin,SharonJ
中科院分区：
文献类型：
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作者：
Kim,Jung;Naqvi,AmmarS;Corbett,RyanJ;Kaufman,RebeccaS;Vaksman,Zalman;Brown,MiguelA;Miller,DanielP;Phul,Saksham;Geng,Zhuangzhuang;Storm,PhillipB;Resnick,AdamC;Stewart,DouglasR;Rokita,JoLynne;Diskin,SharonJ
随着外显子组和全基因组测序率的提高，使用最新的美国医学遗传学会分子病理学协会（ACMG-AMP）标准对大量种系测序变异进行分类的能力至关重要。在这里，我们提出了自动种系变异致病性（AutoGVP），这是一个整合了ClinVar的种系变异致病性注释和修改版InterVar的序列变异分类（PVS1强度调整，去除PP5/BP6）的工具。该工具促进了大规模，临床重点分类生殖系序列变异的研究设置。可用性和实现autogvp是一个用R实现的开源dockerized工作流，可以在GitHub上免费获得https://github.com/diskin-lab-chop/AutoGVP。
SummaryWith the increasing rates of exome and whole genome sequencing, the ability to classify large sets of germline sequencing variants using up-to-date American College of Medical Genetics—Association for Molecular Pathology (ACMG-AMP) criteria is crucial. Here, we present Automated Germline Variant Pathogenicity (AutoGVP), a tool that integrates germline variant pathogenicity annotations from ClinVar and sequence variant classifications from a modified version of InterVar (PVS1 strength adjustments, removal of PP5/BP6). This tool facilitates large-scale, clinically focused classification of germline sequence variants in a research setting.Availability and implementationAutoGVP is an open source dockerized workflow implemented in R and freely available on GitHub at https://github.com/diskin-lab-chop/AutoGVP.