VARiD: A variation detection framework for color-space and letter-space platforms
Adrian V. Dalca; Stephen M. Rumble; Misko Dzamba; Samuel Levy; Michael Brudno
contact: varid [at] cs [dot] toronto [dot] edu
Useful Files
- README (1.0.7e)
- Usage examples (1.0.7c)
- Previous and MATLAB releases
Documents
- VARiD Publication (link | pdf)
Bioinformatics 2010 26(12):i343-i349 - Talk @ ISMB 2010 (pptx | pdf)
- Poster @ ISMB2009 (pptx | pdf)
- Talk @ ISMB2009 SHORT-SIG (pptx | pdf)
- GenomeWeb: No Longer so Short
Article on the state of Short-Read sequencing following ISMB.
Variation Detection with VARiD
Welcome to the website of the VARiD Variation Identification platform.
Description
VARiD is a Hidden Markov Model for SNP and indel identification with AB-SOLiD color-space as well as regular letter-space reads. VARiD combines both types of data in a single framework which allows for accurate predictions. VARiD was developed at the University of Toronto Computational Biology Lab. Please see the publication for more details about the algorithms and the latest README for information regarding installation and usage.
To cite, or learn more about VARiD, please see:
Adrian V. Dalca; Stephen M. Rumble; Samuel Levy; Michael Brudno. VARiD: A variation detection framework for color-space and letter-space platforms. Bioinformatics 2010 26: i343-i349. (link | pdf)
Community
VARiD uses the Google Groups community feature.
- To visit the community click here
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News and Events
05 Oct 2010
Release 1.0.7c
A significantly improved version of VARiD is now released, along with an improved README and usage examples. The helper scripts were also improved.
09 Jun 2010
Release 1.0.0
A new version of VARiD C-code is available, with suppoort for the sam format, new input parameters and several improvements.
07 Jun 2010
Publication
VARiD has appeared in Bioinformatics. (link | pdf)
31 Jan 2010
Release 0.9.9 C
The first official version of VARiD is up on the website. Please see the README for installing and usage instructions.
Please see the download links to the right for obtaining VARiD
18 Jan 2010
Release 0.99 MATLAB
We just released a good, nicely running MATLAB version of the code for VARiD
Please see the download links to the right for obtaining VARiD
07 Jan 2010
Close to release
We hope to release a good version of VARiD, in C, within a week.
28 Jun 2009
Added PDFs
ISMB 2009 Presentation and Poster added below.
25 Jun 2009
Website is up
Please Note that the website and public code is still well under development.
The VARiD code is currently written in MATLAB, currently being translated to C.
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