Snp Viewer


A program for visualising Affymetrix SNP array data

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

Snp Viewer requires as input birdseed files generated by the Affymetrix Genotyping Console (TM) containing the "Call Code" field (i.e. the field giving genotype calls as "AA", "BB", "AB" or "NO CALLS"). If you have these files for your samples of interest you should be good to go.

Currently there is no paper to cite for Snp Viewer, but if you do publish using it please cite the URL "".

SnpViewer was developed by David A. Parry at the University of Leeds.

Snp Viewer showing two samples with overlapping regions of homozygosity Automatically discovered or saved regions shown in green


December 19th, 2013 - Use VCF files in Snp Viewer:

Although Snp Viewer cannot read VCF format files on its own, you can use the script at vcfhacks to convert VCFs to text files that Snp Viewer can read. is a commandline program written in perl and requires you to follow the installation instructions as detailed at vcfhacks.

December 16th, 2013 - Snp Viewer in print:

Snp Viewer's first (to my knowledge) appearance in print, in a Nature Genetics reporting mutations mutations in a regulator of the mitochondrial uniporter:

Loss-of-function mutations in MICU1 cause a brain and muscle disorder linked to primary alterations in mitochondrial calcium signaling. Logan et al., Nature Genetics (2013) doi:10.1038/ng.2851

July 23rd, 2013 - Version 0.9.2 Released

This version includes multiple bug fixes compared to v0.9.1, most relate to the Windows version. If using the installer for Windows it is recommended that you uninstall the previous version using the uninstaller at "C:\Users[your username]\App Data\Local\SnpViewer" before reinstalling. Snp Viewer will appear in your Start Menu in the sub folder "Snp Viewer" rather than "David Parry".

Fixes include:

  • Fixed a problem on all platforms where the interface gets stuck after removing all Affected or all Unaffected samples.
  • Fixed a JavaFX related problem with Windows where the program window resizes slightly during drawing of sample SNPs causing a slightly innacurate image.
  • Fixed an issue with Windows where deletion of files relating to a removed sample might fail.
  • Fixed an issue where failure to delete files would break a project.
  • Check box next to Hide Saved Regions is now more clearly visible.

Many of these issues went unnoticed in the first release because I do not use Windows for day-to-day work. Bug reports for this (or any other platform) are most welcome.