- Unique identifier:
- Command line interface
- Input data:
- The input to the program is one or more DNA sequencing read alignments in BAM format and the capture bait locations or a pre-built “reference” file. All additional data files used in the workflow, such as GC content and the location of sequence repeats, can be extracted from user-supplied genome sequences in FASTA format using scripts included with the CNVkit distribution.
- Apache License version 2.0
- Software type:
- Restrictions to use:
- Operating system:
- Unix/Linux, Mac OS, Windows
- Computer skills:
- Eric Talevich <>
No open topic.
(Talevich et al., 2016)
CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.
PLoS Comput Biol.
PMID: 27100738 DOI: 10.1371/journal.pcbi.1004873
Department of Dermatology, University of California, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
This work was supported by the National Institutes of Health [R01 CA131524, P01 CA025874].
1 user review
1 user review
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!!