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Description
FishingCNV, a GUI software 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 uses a large number of control files and is effective in identifying heterozygous as well as homozygous deletions and amplifications at the resolution of an exon. It should have vast applications in genome research.
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License
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
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