Regenotyping structural variants through an accurate force-calling method

Abstract

Long-read sequencing technologies have great potential for the comprehensive discovery of structural variation (SV). However, accurate genotype assignment for SV is still a challenge due to unavoidable factors, such as specific sequencing errors or limited coverage. Herein, we propose cuteSV2, a fast and accurate long-read-based regenotyping approach that is used to force calling genotypes for given records. In cuteSV2, which is an upgraded version of cuteSV, an improved refinement strategy is applied on the signatures, and the heuristic extracted signatures are purified through spatial and allele similarity estimation. The benchmarking results on several baseline evaluations demonstrate that cuteSV2 outperforms the state-of-the-art methods and is a scalable and robust approach for population studies and clinical practice. cuteSV2 is available at https://github.com/tjiangHIT/cuteSV.