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Short description:
Please summarise the application in a few sentences. Avoid links here. CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Copy number estimation, Structural variation,
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Variant calling, Variant calling,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Illumina,
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
University of California at San Francisco,
== Description == <!-- Describe the application in the space below --> CNVkit is a 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. This method uses the nonspecifically captured off-target reads to supplement read depth information from on-target regions. With relatively simple normalization steps to make these read depths comparable across the genome, CNVkit can produce copy ratio estimates extremely close to those by array CGH. <!-- -->
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