Introduction

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: https://sourceforge.net/projects/fishingcnv/ SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publications

  1. FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data.
    Cite this
    Shi Y, Majewski J, 2013-06-01 - Bioinformatics (Oxford, England)

Credits

  1. Yuhao Shi
    Developer

    Department of Human Genetics, McGill University, Canada

  2. Jacek Majewski
    Investigator

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Summary
AccessionBT002354
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByJacek Majewski