VarFish: comprehensive DNA variant analysis for diagnostics and research
VarFish: comprehensive DNA variant analysis for diagnostics and research
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DOI：
10.1093/nar/gkaa241
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发表时间：
2020-07-02
影响因子：
14.9
通讯作者：
Beule, Dieter
中科院分区：
文献类型：
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作者：
Holtgrewe, Manuel;Stolpe, Oliver;Beule, Dieter
VarFish 是一款用户友好的 Web 应用程序，用于对 DNA 变异数据进行质量控制、过滤、优先级排序、分析和基于用户的注释，重点关注罕见疾病遗传学。它能够处理具有单个或多个样本的变体调用文件。这些变体会自动注释群体频率、分子影响以及 ClinVar 等数据库中的存在情况。此外，它还为致病性评分提供支持，包括 CADD、MutationTaster 和表型相似性评分。用户可以根据这些注释和假定的遗传模式过滤变体，并按这些分数对结果进行排序。通过过滤器的变体会列出其注释以及许多有用的基因组浏览器链接、其他基因/变体数据门户以及用于变体评估的外部工具。 VarFish 允许用户创建自己的注释，包括支持遵循 ACMG-AMP 指南的变异评估。 VarFish 与医疗从业者密切合作，专为诊断和研究环境中的变异分析和优先级排序而设计，如该软件的详细手册中所述。用户界面已针对支持这些协议进行了优化。用户可以在自己的内部服务器上安装 VarFish，它为协作分析提供额外的实验室笔记本功能，并允许重新分析案例，例如更新基因型或表型数据库后。
VarFish is a user-friendly web application for the quality control, filtering, prioritization, analysis, and user-based annotation of DNA variant data with a focus on rare disease genetics. It is capable of processing variant call files with single or multiple samples. The variants are automatically annotated with population frequencies, molecular impact, and presence in databases such as ClinVar. Further, it provides support for pathogenicity scores including CADD, MutationTaster, and phenotypic similarity scores. Users can filter variants based on these annotations and presumed inheritance pattern and sort the results by these scores. Variants passing the filter are listed with their annotations and many useful link-outs to genome browsers, other gene/variant data portals, and external tools for variant assessment. VarFish allows users to create their own annotations including support for variant assessment following ACMG-AMP guidelines. In close collaboration with medical practitioners, VarFish was designed for variant analysis and prioritization in diagnostic and research settings as described in the software's extensive manual. The user interface has been optimized for supporting these protocols. Users can install VarFish on their own in-house servers where it provides additional lab notebook features for collaborative analysis and allows re-analysis of cases, e.g. after update of genotype or phenotype databases.