eHoPASA Files

eHoPASA 0.9

Easy Homozygosity Profiling of Affymetrix SNP Arrays
Copyright 2010 by the Center for Medical Research, Medical University Graz.
Written by Slave Trajanoski.
For questions on EHoPASA, please contact Slave Trajanoski
(slave.trajanoski@medunigraz.at).

1. INTRODUCTION

This program discovers homozygosity regions from an Affymetrix SNP Arrays 
GeneChip® Human Mapping 10K XbaI 142 2.0 and GeneChip® Human Mapping NspI 250K.
Future versions will also support the latest Genome-Wide Human SNP Array 5.0 
and 6.0. The software generates several result text files, which can be used 
for further analysis or plotting diagrams.

2. SYSTEM REQUIREMENTS

At least 1GB of Memory
Windows or Linux Operating System. Macintosh OS should also be supported, but 
it has never been tested.
Java 1.5 JRE

3. INSTALLATION

eHoPASA is distributed under the GNU General Public License.
It is free software; you can redistribute it and/or modify it under the terms 
of the GNU General Public License as published by the Free Software Foundation;
either version 2 of the License or (at your option) any later version.

This program is distributed in the hope that it will be useful, but 
WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY 
or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for 
more details.
Beside own development the software uses one additional library from:
OstermillerUtil Java Utilities Copyright (c) 2001-2007 by Stephen Ostermiller 
and other contributors.

The program requires no installation, since everything is packed in a single 
JAR file. All you need to do is starting the program with the following command:
java -Xmx1024m -jar SNP.jar

4. USE

* Important remark: For this version of the software it is important to sort 
the input Affymetrix data file on chromosome and position coloumn first, 
otherwise the homozygosity regions will not be detected properly.

After program start a window opens with several commands and selections buttons.
First step is to load the input data (single Affymtrix SNP array text file, 
without the first description lines). After data loading you should rewise the 
paramters for the detection of the homozygosity regions:
	a. Homozygosity interval - min size for homozygosity interval
	b. Select confidence - only calls with confidence smaller than selected 
	will be used
	c. Stringency - use or no use of NoCalls (undetermined genotypes)
With the "Select Column" you can choose array for analysis. Depending on the 
computer power it takes few moments for the loding of the data.
Next step is to start the process by clicking the "Start Search" button. Here 
the program asks for name and location of the result file.
eHoPASA generates three result files:
	a. filename.txt
	Here the original data is extended with additional coloumn that shows the 
	number of consecutive homozygous calls greater than "Homozygosity interval".
	b. filename_report.txt
	In the report file only homozygous regions are extracted with the following 
	information:
	Full start call information followed by full end call information, then the 
	new calculated start and end positions including the region size. The last 
	three columns are important for the graphical data presentation.
	c. filename_genotypes.txt
	In this file the genotype data for the detected homozygous regions is 
	presented. The connection between the two datasets can be established
	through the "ID_Genotypes" field.