Difference between revisions of "CNVkit"
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|sw summary=CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. | |sw summary=CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. | ||
|bio domain=Copy number estimation, Structural variation, | |bio domain=Copy number estimation, Structural variation, | ||
− | |bio method=Variant calling, | + | |bio method=Variant calling, Variant calling, |
|bio tech=Illumina, | |bio tech=Illumina, | ||
|created by=Talevich E | |created by=Talevich E |
Latest revision as of 10:43, 11 January 2016
Application data |
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Created by | Talevich E |
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Biological application domain(s) | Copy number estimation, Structural variation |
Principal bioinformatics method(s) | Variant calling, Variant calling |
Technology | Illumina |
Created at | University of California at San Francisco |
Maintained? | Yes |
Input format(s) | BAM, BED |
Output format(s) | BED-like |
Software features | Copy number analysis, data visualization |
Programming language(s) | Python |
Software libraries | Numpy, Biopython, MatPlotLib, Pysam |
Licence | BSD |
Operating system(s) | GNU/Linux, Mac OS X |
Contact: | eric.talevich@ucsf.edu |
Summary: CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.
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Description
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.
Links
References
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