CNVkit: Genome-wide copy number from targeted DNA sequencing

Author:Eric Talevich Contact:eric.talevich@ucsf.edu License:Apache License 2.0 Source code:GitHub Packages:PyPI | Docker | Galaxy | DNAnexus 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
  • Process more tumor samples

Command line usage

• Copy number calling pipeline
  • batch
  • target
  • antitarget
  • coverage
  • reference
  • fix
  • segment
  • call
• Plots and graphics
  • scatter
  • loh
  • diagram
  • heatmap
• Text and tabular reports
  • breaks
  • gainloss
  • gender
  • metrics
  • segmetrics
• Compatibility and other I/O
  • import-picard
  • import-seg
  • export
    • bed
    • cdt, jtv
    • seg
    • nexus-basic
• Additional scripts

FAQ

• File formats
  • BED
  • Target and antitarget bin-level coverages (.cnn)
  • Copy number reference profile (.cnn)
  • Bin-level log2 ratios (.cnr)
  • Segmented log2 ratios (.cns)
• Calling gains and losses
• Tumor heterogeneity
  • Inferring tumor purity and subclonal population fractions
    • Using CNVkit with THetA2
  • Adjusting copy ratios and segments for normal cell contamination
  • Export integer copy numbers as BED
• Whole-genome sequencing and targeted amplicon capture

Python API

• Python API (cnvlib package)
  • Module cnvlib contents
  • Submodules
    • cnarray
    • commands
    • antitarget
    • core
    • coverage
    • diagram
    • export
    • fix
    • importers
    • metrics
    • ngfrills
    • params
    • plots
    • reference
    • reports
    • segmentation
    • smoothing

Citation

We are in the process of publishing a manuscript describing CNVkit. If you use this software in a publication, for now, please cite our preprint manuscript by DOI, like so:

Eric Talevich, A. Hunter Shain, Thomas Botton, Boris C. Bastian (2014) CNVkit: Copy number detection and visualization for targeted sequencing using off-target reads. bioRxiv doi: http://dx.doi.org/10.1101/010876

A poster presentation can be viewed at F1000 Research.

Indices and tables

• Index
• Module Index
• Search Page