标题:Mining structural variants of Heduo12 using paired-end reads
作者:Jia, Huiqiang; Wei, Haicho; Zhu, Daming; Ma, Jingjing; Yang, Hai; Wang, Ruizhi; Feng, Xianzhong
通讯作者:Zhu, DM;Feng, XZ
作者机构:[Jia, Huiqiang; Zhu, Daming; Ma, Jingjing; Yang, Hai; Wang, Ruizhi] Shandong Univ, Sch Comp Sci & Technol, Jinan 250101, Peoples R China.; [Wei, Hai 更多
会议名称:IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM)
会议日期:DEC 15-18, 2016
来源:2016 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM)
出版年:2016
页码:111-115
关键词:Structural variation; Deletion; Insertion; Inversion; Algorithm; Set; cover
摘要:In this paper, we devote to detect those deletions, insertions and inversions, in total of three kinds of structural variations in Heidou12 genome relative to Williams82 genome. We propose two sequencing characteristic based probability models, which use the paired-end reads of Hedou12 and their mapping distribution on Williams82 to evaluate on with what probability a potential structural variant can happen. To reduce the conflicts of those potential structural variants, we propose a set cover problem model to formalize on finding structural variants covering all those reads causing potential structural variants with as high as possible probabilities, and use a primal-dual based algorithm to solve it. The efficiency and feasibility of our algorithm are verified by comparing with DELLY(version0.5.5) and LUMPY (27.12.2014).
收录类别:CPCI-S
资源类型:会议论文
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