Tool: CNVkit, robust genome-wide copy number detection from DNA sequencing
gravatar for Eric T.
3.5 years ago by
Eric T.2.3k
San Francisco, CA
Eric T.2.3k wrote:

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:
Paper (preprint):

cnvkit cnv tool python sv • 1.7k views
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