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sCNAphase is a tool for genotyping copy number variation (CNV) in haplotype resolved whole-genome sequencing data. The sCNAphase algorithm designed is for the analysis of low cellularity aneuploid tumors.


Genetics; Genotype and Phenotype; Oncology


  • Operation: Genotyping
  • Software interface: Command-line user interface
  • Language: C++;R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU Lesser General Public License
  • Cost: Free
  • Version name: 1.4.1
  • Maturity: Stable
  • Credit: Cancer Council Queensland, Cancer Council Queensland.
  • Contact: l.coin _at_
  • Collection: -


Chen W, Robertson AJ, Ganesamoorthy D, Coin LJM "sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors." Nucleic Acids Res. 2017 Mar 17;45(5):e34.
PMID: 27903916
PMCID: PMC5389684

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