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A tool for detection of copy number variation (CNV) in whole-genome exome data from paired or healthy tumor samples. The ADTex algorithm uses Hidden Markov Models (HMM) to predict CNV counts, genotypes, polyploidy, aneuploidy, cell contamination, and baseline shifts. The authors originally named ADTex to CoNVEX, but they changed the name because of the conflict with another tool.


Genetics; sequencing; oncology; Exome sequencing


  • Operation: Statistical calculation; variation detection
  • Input: BAM, BED
  • Output: -
  • Software interface: Command-line user interface
  • Language: Python;R
  • Operating system: Linux
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 2.0
  • Maturity: Mature
  • Credit: Australian Research Council (grant DP1096296). KCA was funded by The University of Melbourne MIFRS and MIRS scholarships.
  • Contact: kaushalyac _at_
  • Collection: -


Amarasinghe KC, Li J, Hunter SM, Ryland GL, Cowin PA, Campbell IG, Halgamuge SK "Inferring copy number and genotype in tumour exome data." BMC Genomics. 2014 Aug 28;15:732.
PMID: 25167919
PMCID: PMC4162913

Amarasinghe KC, Li J, Halgamuge SK "CoNVEX: copy number variation estimation in exome sequencing data using HMM." BMC Bioinformatics. 2013;14 Suppl 2:S2. 2013 Jan 21.
PMID: 23368785
PMCID: PMC3549847

Kaushalya C Amarasinghe, Jason Li, Saman K Halgamuge "Erratum to: CoNVEX: copy number variation estimation in exome sequencing data using HMM" BMC Bioinformaticsvolume 14, Article number: S26 (2013)

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