题目:

Mining structural variants of hedou12 using paired-end reads

作者:

Huiqiang Jia,Haicho Wei,Daming Zhu,Jingjing Ma,Hai Yang,Ruizhi Wang,Xianzhong Feng

刊物名称:

Bioinformatics and Biomedicine

卷期页码:

2017:111-115

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).