CNVkit is a flexible command-line toolkit and Python library for calling, visualizing and analyzing copy number variants or alterations from DNA sequencing reads.

It performs especially well for hybrid capture sequencing protocols with whole-exome or custom target panels, but can also be used on whole-genome sequencing, and there is preliminary support for targeted amplicon capture and direct analysis of SNP allele frequencies.

• Source code: https://github.com/etal/cnvkit
• Documentation: https://cnvkit.readthedocs.org
• Poster: http://f1000.com/posters/browse/summary/1096236
• Paper (preprint): http://dx.doi.org/10.1101/010876