Getting Started

Getting Started with Snp Viewer

First things first

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.

Starting or loading a project

Click the “New Project” button or choose “New Project” from the “File” menu to start a new project. You will be prompted to create a new project file which will consist of your chosen name for the project with an “.svproj” extension. A folder containing important files required for the project will also be created called "(chosen name) SNP View Files".

Any changes to your project will be recorded in the project file automatically. You do not need to save your project manually. If you have a saved project this can be loaded using the
“Load Project” button or “File” menu option instead. Upon starting a project use the “Add Affected” or “Add Unaffected” buttons to add samples to your project. You will be presented with a file chooser dialog from which you can select one or more birdseed files to add to your project.

Interface

Upon loading one or more birdseed files the left hand side of the window will show information about each sample added to the project, with the SNP data presented to the right. The right-hand side of SnpViewer displays one chromosome image at a time. The chromosome can be changed using the dropdown box at the bottom-right of the window. The
default colour-scheme displays “AA” calls in black, “BB” calls in dark grey and “AB” calls in pink. In this manner homozygous regions can be identified as dark areas with very little or no pink while haplotypes can be crudely compared between samples by comparing the black/grey striping for each file. You may change the colour using the dropdown menus towards the bottom-right of the window.

Moving the mouse cursor across the chromosome image will display the corresponding coordinate next to the “Position” label at the bottom of the window. You can select a region for interrogation by holding your mouse button and dragging across the region of interest. A highlighting box will show the region selected and the corresponding start and end coordinates will be displayed in the “Selection” text box at the bottom centre of the window. By right-clicking the selected area you can choose from the pop-up menu to perform various actions such as displaying the flanking SNP IDs, writing the region to an Excel file or adding the region to the project's saved regions.

Finding and Saving Regions

Regions you have identified can be saved as above. Snp Viewer also provides the option for the program to automatically identify homozygous regions present in affected samples and not present in unaffected samples (if provided). This option is provided both for convenience and to help identify regions that may be easily missed by a human, (e.g. because of scaling of larger chromosomes, small overlaps etc.). It is not foolproof nor is it meant to be a complete replacement for examining data by eye. To use this feature either click the “Find Regions” button or select “Find Regions” from the “Regions” menu. You will be presented with a dialog giving a series of options described in detail in the Instructions.pdf document provided on this site.

Zooming Regions

Both selected or saved regions give the option to display a zoomed-in view from their context menus allowing for closer inspection of regions. Similar to the main chromosome view, you may select regions within the zoomed region window and choose to add a new saved region from this selection or write it to an Excel file.

Writing Regions to Excel

You may write all of a project’s saved regions to an Excel spreadsheet using the “Output Saved Regions To File” option from the “Regions” menu. This will produce an Excel (.xlsx)
file with the first sheet containing a summary of all the saved regions and a set of further sheets separated per chromosome showing all the SNP calls for each saved region. Ten SNPs will be added at either end of each region to allow the user to see the start of the flanking heterozygous regions. A single region may also be written to a .xlsx file by right-clicking a selected region, saved region or zoomed region and selecting the relevant menu option.

Drawing and Caching Chromosome Images

By default, each time you change the chromosome viewed, the program will draw the genotypes for each file and cache the generated images to enable quick access for future views. You can use the “Redraw” button to force the program to regenerate the image for a chromosome if, for example, you’ve increased the size of the window a lot and the cached images look fuzzy. If you tick the “Redraw Automatically” checkbox images will always be redrawn fresh. Because caching images can save time when flicking between chromosomes you can use the “Cache Images” button or “File” menu option to cause the program to cache images for all samples and chromosomes for quick access. This process may take a few minutes for several samples or on a low-powered computer. Once done you can quickly look at different chromosomes without having to wait for the program to draw the images.

More

For more detailed instructions including annotated screenshots please download the instructions pdf found here.