FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data

Bioinformatics. 2013 Jun 1;29(11):1461-2. doi: 10.1093/bioinformatics/btt151. Epub 2013 Mar 28.


Summary: Rare copy number variations (CNVs) are frequent causes of genetic diseases. We developed a graphical software package based on a novel approach that can consistently identify CNVs of all types (homozygous deletions, heterozygous deletions, heterozygous duplications) from exome-sequencing data without the need of a paired control. The algorithm compares coverage depth in a test sample against a background distribution of control samples and uses principal component analysis to remove batch effects. It is user friendly and can be run on a personal computer.

Availability and implementation: The main scripts are implemented in R (2.15), and the GUI is created using Java 1.6. It can be run on all major operating systems. A non-GUI version for pipeline implementation is also available. The program is freely available online:

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computer Graphics
  • DNA Copy Number Variations*
  • Exome*
  • Humans
  • Sequence Analysis, DNA*
  • Software*