FishingCNV

FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs.

The program comes in 2 different releases
* GUI version (FishingCNV_X.X.X.zip)
* Command line version (FishingCNV_X.X_pipeline)

Browse through our files to find the different releases.

Features

Graphical User Interface
CNV analysis for matched test/control (e.g. cancer/tumor)
CNV analysis for non-matched samples
Batch-effect removal within the control set
Tab-delimited output can be viewed in Excel
Additional output file can be visualized in IGV
Distribution plots and outlier plots for each chromosome

Project Samples

A typical output file containing putative CNVs ranked by statistical confidence

An overview of CNVs in a typical sample as viewed in IGV

Screen shot of the unpaired analysis feature

Project Activity

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License

GNU General Public License version 3.0 (GPLv3)

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FishingCNV Web Site

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Additional Project Details

Intended Audience

Education, Science/Research

User Interface

Java Swing

Programming Language

Java, S/R

Related Categories

Java Bio-Informatics Software, S/R Bio-Informatics Software

Registered

2012-10-11

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