GASV & GASVPro: Geometric Analysis of Structural Variants

About

GASV and GASVPro are software packages for analysis of structural variation from paired-end sequencing and/or array-CGH data. This software has been tested used to find structural variation in both normal and cancer genomes using data from a variety of next-generation sequencing platforms. It can be used to predict structural variants directly from aligned reads in SAM/BAM format.

GASVPro is a probabilistic version of our original GASV algorithm. GASVPro combines read depth information along with discordant paired-read mappings into a single probabilistic model two common signals of structural variation. When multiple alignments of a read are given, GASVPro utilizes a Markov Chain Monte Carlo procedure to sample over the space of possible alignments.

Downloads

Support

Please see the GASV Google Code site.

For further support, contact gasv [at] cs.brown.edu.

References

The GASVPro algorithm is described in the following paper:

S. Sindi, S. Onal, L. Peng, H. Wu, B.J. Raphael. (2012) An Integrative Probabilistic Model for Identification of Structural Variation in Sequencing Data. Genome Biology 13(3):R22. [Publisher link]

The original GASV method is described in the following paper:

S. Sindi, E. Helman, A. Bashir, B.J. Raphael. (2009) A Geometric Approach for Classification and Comparison of Structural Variants. Bioinformatics. 25: i222-i230. (Special issue for the Joint 17th Annual International >Conference on Intelligent Systems in Molecular Biology and 8th Annual International European Conference on Computational Biology (ISMB/ECCB 09)). [Publisher Link]

Previous versions

These are for archival purposes. It is recommended to download the latest version from link above.

  • Version 1.4 (3/5/2010): Download | Release notes
    What’s new: see release notes

  • Version 1.3 (1/19/2010): Download | Example BAM file
    What’s new: New output formats, streamlining of BAM file handling, bug fixes.

  • Version 1.2 (11/30/2009): Download
    What’s new: Improved handling of SAM/BAM alignment files, speed improvements, maxCliqueSize option.

  • Version 1.1 (10/30/2009): Download
    What’s new: a preprocessor for SAM/BAM files, aCGH comparison, fusion gene detection, and more.