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CNVkit: Genome-wide copy number from targeted DNA sequencing

Author:Eric Talevich
Contact:eric.talevich@ucsf.edu
Source code:GitHub
License:Apache License 2.0
Packages:PyPI | Docker | Galaxy | DNAnexus
Article:PLOS Computational Biology
Q&A:Biostars

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from targeted DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

Command line usage

FAQ & How To

Python API

Citation

If you use this software in a publication, please cite our paper describing CNVkit:

Talevich, E., Shain, A.H., Botton, T., & Bastian, B.C. (2014). CNVkit: Genome-wide copy number detection and visualization from targeted sequencing. PLOS Computational Biology 12(4):e1004873

Also please cite the supporting paper for the segmentation method you use:

PSCBS (cbs, the default):
HaarSeg (haar):
Ben-Yaacov, E., & Eldar, Y.C. (2008). A fast and flexible method for the segmentation of aCGH data. Bioinformatics 24(16):i139-45.
CGH Fused Lasso (flasso):
Tibshirani, R., & Wang, P. (2008). Spatial smoothing and hot spot detection for CGH data using the fused lasso. Biostatistics 9(1):18–29

Who else is using CNVkit?

Google Scholar lists some of the studies where CNVkit has been used by other researchers. We'd like to highlight:

Specific support for CNVkit is included in bcbio-nextgen, THetA2, and MetaSV. CNVkit is also available on the commercial platforms DNAnexus, Bina RAVE, and Diploid InHelix.

Finally, CNVkit can :ref:`export` files to several standard formats that can be used with many other software packages, including BioDiscovery Nexus Copy Number and Integrative Genomics Viewer (IGV).

Indices and tables