Difference between revisions of "CNVkit"
(Added CNVkit) |
m (use EDAM terms) |
||
| Line 1: | Line 1: | ||
{{Bioinformatics application | {{Bioinformatics application | ||
|sw 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. | |sw 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. | ||
| − | |bio domain=Copy number estimation, | + | |bio domain=Copy number estimation, |
| − | |bio method=Structural variation discovery, Variant | + | |bio method=Structural variation discovery, Variant calling, Somatic variant calling, |
| − | |bio tech=Illumina, | + | |bio tech=Illumina, |
|created by=Talevich E | |created by=Talevich E | ||
| − | |created at=University of California at San Francisco, | + | |created at=University of California at San Francisco, |
|maintained=Yes | |maintained=Yes | ||
|email address=eric.talevich@ucsf.edu | |email address=eric.talevich@ucsf.edu | ||
| − | |input format=BAM, BED, | + | |input format=BAM, BED, |
|output format=BED-like | |output format=BED-like | ||
| − | |sw feature=Copy number analysis, data visualization, | + | |sw feature=Copy number analysis, data visualization, |
|language=Python | |language=Python | ||
| − | |library=Numpy, Biopython, MatPlotLib, Pysam, | + | |library=Numpy, Biopython, MatPlotLib, Pysam, |
| − | |licence=BSD, | + | |licence=BSD, |
| − | |os=GNU/Linux, Mac OS X, | + | |os=GNU/Linux, Mac OS X, |
}} | }} | ||
== Description == | == Description == | ||
Revision as of 10:23, 25 August 2015
|
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
References
none specified
To add a reference for CNVkit, enter the PubMed ID in the field below and click 'Add'.
Search for "CNVkit" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
