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cnvHiTSeq is a tool to detect copy number variation (CNV) and genotyping population sequencing data. The cnvHiTSeq algorithm incorporates evidence from the read depth, read pair orientation, split reads, and uses a hidden Markov model to make an integrated analysis of the data from the separate sources.


Genetics; genetic variation


  • Operation: Genetic variation analysis
  • Input: FASTA, BAM
  • Output: -
  • Software interface: Command-line user interface
  • Language: Java
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 0.1.2
  • Credit: UK Biotechnology and Biological Sciences Research Council (BBSRC)
  • Contact: Evangelos Bellos evangelos.bellos09 _at_ | Michael R Johnson m.johnson _at_
  • Collection: -


Bellos E, Johnson MR, Coin LJ "cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data." Genome Biol. 2012 Dec 22;13(12):R120. doi: 10.1186/gb-2012-13-12-r120.
PMID: 23259578
PMCID: PMC4056371

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