CNVkit: Genome-wide copy number from high-throughput sequencing¶
|License:||Apache License 2.0|
|Packages:||PyPI | Docker | Galaxy | DNAnexus|
|Article:||PLOS Computational Biology|
|Consulting:||Contact DNAnexus Science|
CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput 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.
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 and DNAcopy (
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 (
- Ben-Yaacov, E., & Eldar, Y.C. (2008). A fast and flexible method for the segmentation of aCGH data. Bioinformatics 24(16):i139-45.
- pomegranate (HMM segmentation methods):
- Schreiber, J. (2018). pomegranate: Fast and Flexible Probabilistic Modeling in Python. Journal of Machine Learning Research 18(164):1−6.
Command line usage¶
- Copy number calling pipeline
- Plots and graphics
- Text and tabular reports
- Compatibility and other I/O
- RNA expression
- Additional scripts
- File formats
- Allele frequencies and copy number
- Bias corrections
- Chromosomal sex
- Calling copy number gains and losses
- Tumor analysis
- Tumor heterogeneity
- Germline analysis
- Whole-genome sequencing and targeted amplicon capture