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¶
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): - Olshen, A.B., Bengtsson, H., Neuvial, P., Spellman, P.T., Olshen, R.A., & Seshan, V.E. (2011). Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics 27(15):2038–46.
- Venkatraman, E.S., & Olshen, A.B. (2007). A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23(6):657–63
- 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:
- McCreery, M.Q. et al. (2015). Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers. Nature Medicine 21, 1514–1520
- Shain, A.H. et al. (2015). Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway. Nature Genetics, 47(10), 1194-1199
- Shain, A.H. et al. (2015). The Genetic Evolution of Melanoma from Precursor Lesions. New England Journal of Medicine, 373(20), 1926-1936
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 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).