Snp Viewer Files

SnpViewer v0.9.1

SnpViewer aims to be a simple, easy-to use program that enables the viewing and analysis of Affymetrix SNP chip data for autozygosity mapping.

Installation

Mac OS X: Download the SnpViewer-MacOSX-0.9.1.dmg Disk Image. Double click the downloaded Disk Image and drag the SnpViewer icon into the Applications folder. On Mac OS X 10.8 (Mountain Lion) you may need to ensure that you allow applications from unidentified developers by going to “System Preferences”, clicking “Security & Privacy” and below the heading “Allow applications downloaded from:” selecting “Anywhere”. This simply allows you to install my application on your machine without me having to pay Apple a fee to get a code-signing ID.

Windows installer: Download and open the “SnpViewer-0.9.1-Windows64bit-installer.exe” file. Once finished, SnpViewer should be available from your Start menu. If you need to locate the installation directory (e.g. to uninstall or if you remove the Start menu shortcut) the folder should be located at “C:\Users[your username]\App Data\Local\SnpViewer”.

Windows zip file: Download and extract the SnpViewer-Windows64bit-0.9.1.zip file and extract in a directory of your choosing. Double-click the extracted SnpViewer.exe to run.

Linux deb: Install using ‘sudo dpkg -i SnpViewer-0.9.1.x86_64_linux.deb’. Graphical install also works fine on debian using gdebi. Ubuntu’s Software Centre will complain about the .deb but will install fine if you choose the “ignore and install” option. The executable will be installed to “/opt/SnpViewer” and a .desktop file created in “/usr/share/applications”. To uninstall use ‘sudo apt-get remove snpviewer’.

Linux RPM: Use ‘sudo rpm -ivh SnpViewer-0.9.1.x86_64_linux.rpm’ to install or whatever graphical front-end you have on your system. Remove using ‘sudo rpm -ev SnpViewer’ or ‘yum remove SnpViewer’.

Linux tarballs: Extract the tar.bz2 file in a directory of your choosing and run the executable from the newly created SnpViewer directory.

jar_file: Extract the archive and run the SnpViewer.jar file using the command 'java -jar SnpViewer.jar'. Set memory requirements using the -Xms and -Xmx arguments. You will need a java runtime that supports javafx.

SnpViewer

Currently only human genomes hg19/b37 and hg18/b36 are supported. SnpViewer also currently requires input files to be in the birdseed format as produced by Affymetrix Genotyping Console containing the "Chromosome", "Chromosomal Position", "Call Codes", "dbsnp rs id" fields. Support for other formats may be added if there is sufficient demand.

SnpViewer was developed by David A. Parry in spare time. I'm a geneticist/molecular biologist at the University of Leeds with no formal training in programming or computer science but have made this program in the hope that it is useful for people like me who often make use of autozygosity mapping in genetic studies, have fairly simple requirements of their analysis programs and would like to be able to run their program on various different operating systems.

If you find this program useful and use it for a paper ***please cite the URL https://sourceforge.net/projects/snpviewer/ ***

Thanks!

Snp Viewer - a program for viewing SNP data and identifying regions of homozygosity

Copyright (C) 2013 David A. Parry

d.a.parry@leeds.ac.uk | https://sourceforge.net/projects/snpviewer/

This program 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 3 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.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.