CNVkit specifications

Unique identifier:
OMICS_11538
Interface:
Command line interface
Input data:
The input to the program is one or more DNA sequencing read alignments in BAM format and the capture bait locations or a pre-built “reference” file. All additional data files used in the workflow, such as GC content and the location of sequence repeats, can be extracted from user-supplied genome sequences in FASTA format using scripts included with the CNVkit distribution.
License:
Apache License version 2.0
Stability:
Stable
Maintained:
Yes
Software type:
Toolkit/Suite
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Requirements:
Python

versioning

tutorial arrow
×
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

CNVkit distribution

download

CNVkit support

Documentation

Maintainer

  • Eric Talevich <>

forum

tutorial arrow
×
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

Credits

tutorial arrow
×
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship

Publications

Institution(s)

Department of Dermatology, University of California, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA

Funding source(s)

This work was supported by the National Institutes of Health [R01 CA131524, P01 CA025874].

User review

tutorial arrow
×
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community
Sort by:

1 user review

star_border star_border star_border star_border star_border
star star star star star

1 user review

star_border star_border star_border star_border star_border
star star star star star
Antoine Rousselin's avatar image Antoine Rousselin's country flag

Antoine Rousselin

star_border star_border star_border star_border star_border
star star star star star

I have been using this tool since 2017 for the detection of CNV in genes predisposed to breast and ovarian cancer.
This software is very precise (specificity, sensitivity). I'm now using it in diagnostics, on small and large panels of genes.
the documentation is rich and well done. Recommended for immediate use!!

Related Tools