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A tool for detection of somatic copy-number variation in tumor sample data. The DEFOR algorithm accounts for coverage, allele frequencies, and allows large-scale copy-number variation (CNV).


Medicine; Oncology; Molecular genetics; DNA polymorphism; DNA mutation


  • Operation: Genetic variation analysis; Structural variation discovery
  • Input: mpileup; BAM; SAM
  • Output: -
  • Software interface: Command-line user interface
  • Language: C;Perl
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Maturity: Emerging
  • Credit: Cancer Prevention and Research Institute of Texas, the National Institutes of Health (NIH)
  • Contact: He Zhang he.zhang _at_
  • Collection: -


Zhang H, Zhan X, Brugarolas J, Xie Y "DEFOR: depth- and frequency-based somatic copy number alteration detector." Bioinformatics. 2019 Oct 1;35(19):3824-3825.
PMID: 30860569
PMCID: PMC6761943

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