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An R package AluScanCNV2 is based on the previously developed AluScanCNV tool. This tool is specifically designed for copy number variation (CNV) calling from next-generation sequencing (NGS) data and for germline CNV-based cancer risk prediction. It uses Geary-Hinkley transformation (GHT)-based comparison of the read-depth.


Genetics; sequencing; Oncology; machine learning


  • Operation: Copy number estimation; Variant calling
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Linux; Max OS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: 2
  • Maturity: Mature
  • Credit: H. Xue from University Grants Committee (VPRDO09/10.SC08), and Innovation and Technology Fund (ITS/113/15FP) of Hong Kong SAR.
  • Contact: hxue _at_
  • Collection: -


Hu T, Chen S, Ullah A, Xue H "AluScanCNV2: An R package for copy number variation calling and cancer risk prediction with next-generation sequencing data." Genes Dis. 2018 Sep 8;6(1):43-46.
PMID: 30906832
PMCID: PMC6411622

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