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A tool for the detection of copy number variation (CNV) in single nucleotide polymorphism (SNP) arrays, particularly designed for germline data. SegCNV supports Illumina 550K and 610K genotyping platforms. The algorithm uses log R ratios (LRR) and B allele frequencies (BAF) for the detection.


Genotype and phenotype; DNA polymorphism; Genetics; DNA mutation


  • Operation: Copy number estimation
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux
  • License: Other
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: The Intramural ResearchProgram, Division of Cancer Epidemiology and Genetics, National Cancer Institute at the National Institutes of Health, Autism Genetic Resource Exchange (AGRE) Con-sortium and the participating AGRE families, the Biowulf Linux cluster at the National Institutes of Health, Bethesda, MD.
  • Contact: jianxin.shi _at_
  • Collection: -


Shi J, Li P "An integrative segmentation method for detecting germline copy number variations in SNP arrays." Genet Epidemiol. 2012 May;36(4):373-83.
PMID: 22539397

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