Changepoint Analysis for Efficient Variant Calling

  • Adam Bloniarz
  • Ameet Talwalkar
  • Jonathan Terhorst
  • Michael I. Jordan
  • David Patterson
  • Bin Yu
  • Yun S. Song
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8394)


We present CAGe, a statistical algorithm which exploits high sequence identity between sampled genomes and a reference assembly to streamline the variant calling process. Using a combination of changepoint detection, classification, and online variant detection, CAGe is able to call simple variants quickly and accurately on the 90-95% of a sampled genome which differs little from the reference, while correctly learning the remaining 5-10% that must be processed using more computationally expensive methods. CAGe runs on a deeply sequenced human whole genome sample in approximately 20 minutes, potentially reducing the burden of variant calling by an order of magnitude after one memory-efficient pass over the data.


genome complexity next-generation sequencing variant calling changepoint detection 


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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Adam Bloniarz
    • 1
  • Ameet Talwalkar
    • 2
  • Jonathan Terhorst
    • 1
  • Michael I. Jordan
    • 1
    • 2
  • David Patterson
    • 2
  • Bin Yu
    • 1
  • Yun S. Song
    • 1
    • 2
    • 3
  1. 1.Department of StatisticsUniversity of CaliforniaBerkeleyUSA
  2. 2.Computer Science DivisionUniversity of CaliforniaBerkeleyUSA
  3. 3.Department of Integrative BiologyUniversity of CaliforniaBerkeleyUSA

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