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 | SeqAnswers

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.

• Quick start
  • Install CNVkit
  • Download the reference genome
  • Map sequencing reads to the reference genome
  • Build a reference from normal samples and infer tumor copy ratios
  • Next steps

Command line usage

• Copy number calling pipeline
  • batch
  • target
  • access
  • antitarget
  • coverage
  • reference
  • fix
  • segment
  • call
• Plots and graphics
  • scatter
  • diagram
  • heatmap
  • Customizing plots
• Text and tabular reports
  • breaks
  • gainloss
  • gender
  • metrics
  • segmetrics
• Compatibility and other I/O
  • version
  • import-picard
  • import-seg
  • import-theta
  • export
• Additional scripts

FAQ & How To

• Calling copy number gains and losses
• Tumor analysis
• Tumor heterogeneity
  • Estimating tumor purity and normal contamination
  • Inferring tumor purity and subclonal population fractions from sequencing
  • Adjusting copy ratios and segments for normal cell contamination
  • Export integer copy numbers as BED or VCF
• Germline analysis
• Whole-genome sequencing and targeted amplicon capture
  • Whole-Genome Sequencing (WGS)
  • Targeted Amplicon Sequencing (TAS)
• Gender
  • Reference gender
  • Gender in calling absolute copy number
  • Plots and gender
  • FAQ
• Bias corrections
  • GC content
  • Sequence repeats
  • Targeting density
• File formats
  • BED and GATK/Picard Interval List
  • VCF
  • Target and antitarget bin-level coverages (.cnn)
  • Copy number reference profile (.cnn)
  • Bin-level log2 ratios (.cnr)
  • Segmented log2 ratios (.cns)

Python API

• Python API (cnvlib package)
  • Module cnvlib contents
  • Core classes
  • Interface to CNVkit sub-commands
  • Helper modules

Citation

We have published a paper describing CNVkit. If you use this software in a publication, please cite:

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

A poster presentation can be viewed at F1000 Research.

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).

Indices and tables

• Index
• Module Index
• Search Page