Split-Read Indel and Structural Variant Calling Using PINDEL

  • Kai YeEmail author
  • Li Guo
  • Xiaofei Yang
  • Eric-Wubbo Lamijer
  • Keiran Raine
  • Zemin Ning
Part of the Methods in Molecular Biology book series (MIMB, volume 1833)


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.

Key words

PINDEL Split-read Structural variants 



The authors gratefully acknowledge the financial support from General Program of National Natural Science Foundation of China (No. 31671372, 61702406).


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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Kai Ye
    • 1
    • 2
    • 3
    • 4
    Email author
  • Li Guo
    • 1
  • Xiaofei Yang
    • 1
  • Eric-Wubbo Lamijer
    • 1
  • Keiran Raine
    • 5
  • Zemin Ning
    • 5
  1. 1.MOE Key Lab for Intelligent Networks & Network SecurityXi’an Jiaotong UniversityXi’anChina
  2. 2.School of Electronics and Information EngineeringXi’an Jiaotong UniversityXi’anChina
  3. 3.The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anChina
  4. 4.Collaborative Innovation Center for Genetics and Development, School of Life SciencesFudan UniversityShanghaiChina
  5. 5.Wellcome Trust Sanger InstituteHinxtonUK

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