intansv: an R package for integrative analysis of structural variations

Lihua Jia; Na Liu; Fangfang Huang; Zhengfu Zhou; Xin He; Haoran Li; Zhizhan Wang; Wen Yao

doi:10.7717/peerj.8867

intansv: an R package for integrative analysis of structural variations

PeerJ. 2020 Apr 28:8:e8867. doi: 10.7717/peerj.8867. eCollection 2020.

Authors

Lihua Jia^#^{1

2}, Na Liu^#¹, Fangfang Huang¹, Zhengfu Zhou³, Xin He¹, Haoran Li¹, Zhizhan Wang¹, Wen Yao^{1

4}

Affiliations

¹ National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, China.
² National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China.
³ Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China.
⁴ National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei, China.

^# Contributed equally.

Abstract

Identification of structural variations between individuals is very important for the understanding of phenotype variations and diseases. Despite the existence of dozens of programs for prediction of structural variations, none of them is the golden standard in this field and the results of multiple programs were usually integrated to get more reliable predictions. Annotation and visualization of structural variations are important for the understanding of their functions. However, no program provides these functions currently as far as we are concerned. We report an R package, intansv, which can integrate the predictions of multiple programs as well as annotate and visualize structural variations. The source code and the help manual of intansv is freely available at https://github.com/venyao/intansv and http://www.bioconductor.org/packages/devel/bioc/html/intansv.html.

Keywords: Genome variation; Integrative analysis; Next-generation sequencing; R package; Structural variation; Visualization.

Grants and funding

This research was supported by the research start-up fund of Henan Agricultural University (30500581), the Scientific and Technological Project of Henan Province (182102110278), the Project of Henan Provincial Department of Education (18A210017) and the open funds of the National Laboratory of Wheat Engineering, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huang-huai Region, Ministry of Agriculture, Henan Key Laboratory of Wheat Biology. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.