CNVkit

Application data
Created by	Talevich E
Biological application domain(s)	Copy number estimation
Principal bioinformatics method(s)	Structural variation discovery, Variant Calling, Somatic 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. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina.

"Error: no local variable "counter" was set." is not a number.

Description

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

• CNVkit Source code [ edit link ]
• CNVkit Manual [ edit link ]

• Add a Link

References

none specified

To add a reference for CNVkit, enter the PubMed ID in the field below and click 'Add'.

 

[ edit box ]

Search for "CNVkit" in the SEQanswers forum / BioStar or:

Web Search	Wiki Sites	Scientific
Google. Bioinformatics journals Clusty	WikiPedia MetaBase BioPedia OpenWetWare bifx wiki	PubMed Europe PMC ScientificCommons.org