title: FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  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: https://sourceforge.net/projects/fishingcnv/
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Human Genetics, McGill University, Montreal, Quebec, Canada. yuhao.shi@mail.mcgill.ca
authors.forename: Yuhao
authors.initials: Y
authors.lastname: Shi
authors.forename: Jacek
authors.initials: J
authors.lastname: Majewski
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D056915:DNA Copy Number Variations; D059472:Exome; D006801:Humans; D017422:Sequence Analysis, DNA; D012984:Software