Guo Qingxiang, Li Yangyang, Wang Ting-You, Ramakrishnan Abhi, Yang Rendong
Department of Urology, Northwestern University Feinberg School of Medicine, 303 E Superior St, Chicago, 60611, IL, USA.
Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 675 N St Clair St, Chicago, 60611, IL, USA.
bioRxiv. 2025 Mar 28:2025.03.24.645012. doi: 10.1101/2025.03.24.645012.
Structural variants (SVs) significantly influence genomic variability and disease, but their accurate analysis across multiple samples and sequencing platforms remains challenging. We developed OctopusV, a tool that standardizes ambiguous breakend (BND) annotations into canonical SV types (inversions, duplications, translocations) and integrates variant calls using flexible set operations, such as union, intersection, difference, and complement, enabling cohort-specific variant identification. Together with TentacleSV, an automated pipeline, OctopusV provides an end-to-end solution from raw data to final callsets. Evaluations show improved precision, recall, and consistency, highlighting its value in cancer genomics and rare disease diagnostics. Both tools are available at https://github.com/ylab-hi/OctopusV and https://github.com/ylab-hi/TentacleSV.
结构变异（SVs）对基因组变异性和疾病有重大影响，但其在多个样本和测序平台上的准确分析仍然具有挑战性。我们开发了OctopusV，这是一种将模糊断点（BND）注释标准化为标准SV类型（倒位、重复、易位）的工具，并使用灵活的集合操作（如并集、交集、差集和补集）整合变异调用，从而实现特定队列的变异识别。OctopusV与自动化流程TentacleSV一起，提供了从原始数据到最终调用集的端到端解决方案。评估显示其精度、召回率和一致性均有所提高，突出了其在癌症基因组学和罕见病诊断中的价值。这两个工具均可在https://github.com/ylab-hi/OctopusV和https://github.com/ylab-hi/TentacleSV上获取。
