This is the Linux app named FishingCNV to run in Linux online whose latest release can be downloaded as FishingCNV_1.5.3.zip. It can be run online in the free hosting provider OnWorks for workstations.
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FishingCNV to run in Linux online
DESCRIPTION
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
Audience
Science/Research, Education
User interface
Java Swing
Programming Language
Java, S/R
This is an application that can also be fetched from https://sourceforge.net/projects/fishingcnv/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.