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CLImAT-HET is a tool for the detection of subclonal copy number variation (CNV) and loss of heterozygosity in tumor samples. The CLImAT-HET algorithm uses whole-genome sequencing (WGS) data and a factorial hidden Markov model.


Genetics; Whole genome sequencing; DNA structural variation; Oncology


  • Operation: Polymorphism detection; Sequence analysis; Structural variation detection
  • Software interface: Command-line user interface
  • Language: C;Matlab
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU GPL v2
  • Cost: Free
  • Version name: 1.0.0
  • Credit: National Natural Science Foundation of China
  • Contact: Zhenhua Yu yzh163 _at_
  • Collection: -


Yu Z, Li A, Wang M "CLImAT-HET: detecting subclonal copy number alterations and loss of heterozygosity in heterogeneous tumor samples from whole-genome sequencing data." BMC Med Genomics. 2017 Mar 15;10(1):15.
PMID: 28298214
PMCID: PMC5351278

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