Geometric Analysis of Structural Variants (GASV)

Software for identifying and comparing structural variants by computing 
intersections of breakpoint regions.

If you use GASV in your research, please cite: 
S. Sindi, E. Helman, A. Bashir, B.J. Raphael. A Geometric Approach for
Classification and Comparison of Structural Variants. Joint: 17th
Annual International Conference on Intelligent Systems in Molecular
Biology and 8th Annual International European Conference on
Computational Biology (ISMB/ECCB 09).  Bioinformatics 2009
25(12):i222-i230. 

This product includes software developed by the Solution Engineering,
Inc. (http://www.seisw.com/). 

Contact: Ben Raphael at gasv@cs.brown.edu

Version: 1.4
Version Date: Mar 5 2010

SUMMARY ==============================================

This README file lists and annotates the files distributed
with GASV Release 1.4, GASV_RELEASE_1.4.tar.gz.

CONTENTS =============================================

(i) Documentation:

* Quickstart Guide; GASV_Quickstart_Guide.txt
	A quick introduction to GASV going from the 
	example BAM file "Example.bam" to a set of predicted
	structural variants. The Example.bam is available
	as a separate download.

* GASV Manual; MANUAL.txt	
	A complete description of GASV features and options.

* BAM Preprocessor Documentation; BAM_preprocessor.txt
	Detailed description of BAM_preprocessor.pl, used
	to convert from the BAM format to GASV input format.

* GASV Release Notes; RELEASE_NOTES.txt
	Documentation of features, options developed with each GASV 
	Release.

* GASV FAQ; FAQ.txt
	A list of "Frequently Asked Questions" regarding GASV.

(ii) GASV Software: gasv.jar

(iii) Preprocessors to convert from BAM/MAQ to GASV input files:
	- BAM Preprocessor:
		install.sh, BAM_preprocessor.pl, generate_GASV.pl,
		LminLmaxProcessor_Source/
	- MAQ Preprocessor:
		Maq_preprocessor/

(iv) Example Files:

* Example ESP Files: Cancer, sample 

* Example CGH file: sampleCGH 

* Example Batch Input Files: sample.in, Cancer.in, sampleCGH.in