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DECA

DECA

A tool to call copy-number variation (CNV) with ADAM and Apache Spark. The DECA algorithm implements XHMM, including new optimizations, to speed up the computation. It also uses the Viterbi algorithm in logs space and scaled versions of the forward and backward algorithms. Requires: Maven, Spark 2.1.0+, Hadoop 2.7, Scala 2.11.

Topic

DNA structural variation; Genetic variation;

Details

  • Operation: Copy number estimation
  • Software interface: Command-line user interface
  • Language: Java;Scala
  • Operating system: Linux
  • License: Apache 2.0 license
  • Cost: Free
  • Version name: 0.2.0
  • Maturity: Emerging
  • Credit: Middlebury College, National Science Foundation (NSF), Lawrence Berkeley National Laboratory (LBNL), The Defense Advanced Research Projects Agency (DARPA)
  • Contact: xinglong.wang _at_ manchester.ac.uk
  • Collection: -

Publications

Linderman MD, Chia D, Wallace F, Nothaft FA "DECA: scalable XHMM exome copy-number variant calling with ADAM and Apache Spark." BMC Bioinformatics. 2019 Oct 11;20(1):493. https://doi.org/10.1186/s12859-019-3108-7
PMID: 31604420
PMCID: PMC6787990


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