CNVkit specifications

Information


Unique identifier OMICS_11538
Name CNVkit
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data One or more DNA sequencing read alignments and the capture bait locations or a pre-built “reference” file.
Input format BAM
Operating system Unix/Linux, Mac OS, Windows
License Apache License version 2.0
Computer skills Advanced
Version 0.9.5
Stability Stable
Requirements Biopython, Reportlab, matplotlib, NumPy, SciPy, Pandas, pyfaidx, pysam, DNAcopy, cghFLasso
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Eric Talevich <>

Publications for CNVkit

CNVkit institution(s)
Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; Department of Dermatology, University of California, San Francisco, CA, USA
CNVkit funding source(s)
Supported by the National Institutes of Health [R01 CA131524, P01 CA025874].

CNVkit review

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Antoine Rousselin

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Desktop
I have been using this tool since 2017 for the detection of CNV in genes predisposed to breast and ovarian cancer.
This software is very precise (specificity, sensitivity). I'm now using it in diagnostics, on small and large panels of genes.
the documentation is rich and well done. Recommended for immediate use!!