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Despite the availability of numerous SV callers and efforts to merge SVs from multiple tools, there remains limited research on quantifying the confidence levels for the reported results. In this work, we propose a Bayesian integration model that combines SV calls from different tools. Notably, we introduce an approach for false discovery rate (FDR) control and provide a quantitative measure for the merged SVs. Our model can handle cases where certain tools lack quality scores, showcasing its flexibility in incorporating additional tools. Through extensive simulation studies, we evaluate the performance of our method under various conditions, demonstrating the FDR estimation accuracy and improved F1 score. Furthermore, we validate our model using simulated human genome sequencing data and the HG002\u00a0dataset.<\/jats:p>","DOI":"10.1002\/bimj.70128","type":"journal-article","created":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T10:03:02Z","timestamp":1774605782000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Bayesian Integrative Detection of Structural Variations With False Discovery Rate Control"],"prefix":"10.1002","volume":"68","author":[{"given":"Sheng","family":"Lian","sequence":"first","affiliation":[{"name":"Department of Electronic and Computer Engineering The Hong Kong University of Science and Technology, Clear Water Bay Hong Kong China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5178-8470","authenticated-orcid":false,"given":"Jiandong","family":"Shi","sequence":"additional","affiliation":[{"name":"Department of Electronic and Computer Engineering The Hong Kong University of Science and Technology, Clear Water Bay Hong Kong China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingyu","family":"Hao","sequence":"additional","affiliation":[{"name":"Department of Electronic and Computer Engineering The Hong Kong University of Science and Technology, Clear Water Bay Hong Kong China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Electronic and Computer Engineering The Hong Kong University of Science and Technology, Clear Water Bay Hong Kong China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongyi","family":"Luo","sequence":"additional","affiliation":[{"name":"Department of Statistics and Data Science The Chinese University of Hong Kong, Shatin, N.T. 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