CNVkit specifications

Information


Unique identifier OMICS_11538
Name CNVkit
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
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.
Operating system Unix/Linux, Mac OS, Windows
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Requirements Python
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Eric Talevich <>

CNVkit article

CNVkit institution(s)
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
CNVkit funding source(s)
This work was supported by the National Institutes of Health [R01 CA131524, P01 CA025874].

CNVkit review

star_border star_border star_border star_border star_border
star star star star star

Antoine Rousselin

star_border star_border star_border star_border star_border
star star star star star
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!!