UNIT 15.6 BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping

  1. Xian Fan1,
  2. Travis E. Abbott2,
  3. David Larson2,
  4. Ken Chen1

Published Online: 21 MAR 2014

DOI: 10.1002/0471250953.bi1506s45

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Fan, X., Abbott, T. E., Larson, D. and Chen, K. 2014. BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping. Current Protocols in Bioinformatics. 15:15.6:15.6.1–15.6.11.

Author Information

  1. 1

    Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas

  2. 2

    The Genome Institute at Washington University, St. Louis, Missouri

Publication History

  1. Published Online: 21 MAR 2014


The advent of next-generation sequencing data has made it possible to cost-effectively detect and characterize genomic variation in human genomes. Structural variation, including deletion, duplication, insertion, inversion, and translocation, is of great importance to human genetics due to its association with many genetic diseases. BreakDancer is a bioinformatics tool that relates paired-end read alignments from a test genome to the reference genome for the purpose of comprehensively and accurately detecting various types of structural variation. Curr. Protoc. Bioinform. 45:15.6.1-15.6.11. © 2014 by John Wiley & Sons, Inc.


  • genomics;
  • next-generation sequencing;
  • BreakDancer;
  • structural variation;
  • discordant read pair