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An updated version of matchclips for detecting copy number variation (CNV) breakpoints. The algorithm identified the breakpoint CIGAR strings of reads and their positions. The updated algorithm runs much faster than the original one.


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: -
  • 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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