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A legacy tool for detecting copy number variation (CNV) breakpoints. The algorithm identified the breakpoint CIGAR strings of reads and their positions. See links for the updated version.


Biology; Genetics


  • Operation: Variation detection
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: -
  • Maturity: Legacy
  • Credit: NIH grants CA127334, GM097525, EY020483 and EY021451.
  • Contact: Hongzhe Li hongzhe _at_
  • Collection: -


Wu Y, Tian L, Pirastu M, Stambolian D, Li H "MATCHCLIP: locate precise breakpoints for copy number variation using CIGAR string by matching soft clipped reads." Front Genet. 2013 Aug 16;4:157.
PMID: 23967014
PMCID: PMC3744852

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