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CloneCNA is a tool to detect copy number variation (CNV) in heterogeneous tumor samples in whole-genome exome sequencing data. The CloneCNA algorithm identifies clonal and subclonal CNVs by computing the log-ratio of the read counts of paired healthy samples and tumor B allele frequencies in germline at independent SNP locations.


Genetics; molecular genetics; human genetics; genetic variation; Oncology


  • Operation: Variation detection
  • Software interface: Command-line user interface
  • Language: C++;Matlab
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: 2.0
  • Credit: National Natural Science Foundation of China.
  • Contact: Zhenhua Yu yzh163 _at_ | Ao Li, Associate Professor, Department of Electronic Science and Technology, USTC aoli _at_
  • Collection: -


Yu Z, Li A, Wang M "CloneCNA: detecting subclonal somatic copy number alterations in heterogeneous tumor samples from whole-exome sequencing data." BMC Bioinformatics. 2016 Aug 19;17:310.
PMID: 27538789
PMCID: PMC4990858

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