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SAAS-CNV is a tool to identify somatic copy number variation (CNV) in next-generation sequencing (NGS) data. The SAAS-CNV algorithm consists of four main steps: (1) reading a reference and alleles at each locus for comparison of the read depth and alleles with tumor and healthy samples, (2) joint segmentation on the two signals, (3) correction of the CNV baseline, (4) calling of somatic CNVs for all detected signals.


Genetics; DNA structural variation; Oncology


  • Operation: Polymorphism detection; Sequence analysis; Structural variation detection
  • Input: VCF
  • Output: -
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU GPL 2
  • Cost: Free
  • Version name: 0.3.4
  • Maturity: Stable
  • Credit: National Natural Science Foundation of China, Melanoma Research Foundation.
  • Contact: Zhongyang Zhang zhongyang.zhang _at_ | Ke Hao ke.hao _at_
  • Collection: -


Zhang Z, Hao K "SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data." PLoS Comput Biol. 2015 Nov 19;11(11):e1004618. eCollection 2015 Nov.
PMID: 26583378
PMCID: PMC4652904

Zhang Z, Hao K "Using SAAS-CNV to Detect and Characterize Somatic Copy Number Alterations in Cancer Genomes from Next Generation Sequencing and SNP Array Data." Methods Mol Biol. 2018;1833:29-47.
PMID: 30039361

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