Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

Download and Installation

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Sanger Contributors
External Contributors


  • Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.

    Ye K, Schulz MH, Long Q, Apweiler R and Ning Z

    Bioinformatics (Oxford, England) 2009;25;21;2865-71

  • A comprehensive catalogue of somatic mutations from a human cancer genome.

    Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ et al.

    Nature 2010;463;7278;191-6

  • Detecting Break Points of Insertions and Deletions from Paired-end Short Reads

    Kai Ye and Zemin Ning

    Next-generation Sequencing: Current Technologies and Applications 2014

Tool Type