Split-Read Indel and Structural Variant Calling Using PINDEL

Kai Ye; Li Guo; Xiaofei Yang; Eric-Wubbo Lamijer; Keiran Raine; Zemin Ning

doi:10.1007/978-1-4939-8666-8_7

Split-Read Indel and Structural Variant Calling Using PINDEL

Methods Mol Biol. 2018:1833:95-105. doi: 10.1007/978-1-4939-8666-8_7.

Authors

Kai Ye^{1

2

3

4}, Li Guo⁵, Xiaofei Yang⁵, Eric-Wubbo Lamijer⁵, Keiran Raine⁶, Zemin Ning⁶

Affiliations

¹ MOE Key Lab for Intelligent Networks & Network Security, Xi'an Jiaotong University, Xi'an, China. kaiye@xjtu.edu.cn.
² School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an, China. kaiye@xjtu.edu.cn.
³ The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China. kaiye@xjtu.edu.cn.
⁴ Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China. kaiye@xjtu.edu.cn.
⁵ MOE Key Lab for Intelligent Networks & Network Security, Xi'an Jiaotong University, Xi'an, China.
⁶ Wellcome Trust Sanger Institute, Hinxton, UK.

PMID: 30039366
DOI: 10.1007/978-1-4939-8666-8_7

Abstract

Genetic variations are important evolutionary forces in all forms of life in nature. Accurate and efficient detection of various forms of genetic variants is crucial for understanding cell function, evolution and diseases in living organisms. In this chapter, we describe a detailed protocol that uses Pindel, a split-read algorithm, to discover indels and structural variants in a given genome, from Illumina short-read sequencing data produced from biological samples.

Keywords: PINDEL; Split-read; Structural variants.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Genetic Variation*
Genome*
Sequence Analysis, DNA / methods*