To view whole genome analysis scan results in Haploview, you will first need to download the latest beta version of Haploview 4.0 at http://www.broadinstitute.org/ftp/pub/mpg/haploview/. Once there, you will be asked to provide your email address so that we can keep you informed of important beta updates. After entering your email, you will be directed to a link which you can use to download the latest beta version of Haploview 4.0. Save the JAR file to a location on your hard drive. Haploview is a java program and as such you will also need the java runtime environment which can be found at http://java.sun.com/downloads/index.html if you do not already have it installed on your system.
Once you have the JAR file, download the results file and map file and save them to the same file as the Haploview JAR file that you downloaded earlier. Double click on the Haploview JAR file to run the program. You should see a “Welcome to Haploview” (Figure 1 below) dialog on your screen with six tabs along the left-hand side.
Figure 1: Welcome to Haploview
Click the last tab entitled “PLINK Format”. Use the “Browse” buttons next to the “Results File” and “Map File” fields to browse to the appropriate files that you downloaded earlier. Once you have selected the files, click the “OK” button on the bottom of the dialog.
Depending on the size of the dataset that you are viewing, Haploview may take a minute or two to load in the data. Once it is loaded, you will see a table within a tab designated as “PLINK”. The table should contain one row for each result in your dataset. You can sort any column in the table by clicking on the column header. Click once to sort ascending, twice for descending, and a third time to reset the column back to its unsorted state. Keep in mind that for large datasets, these sort operations may take some time.
At the bottom of your screen, you will see a panel with a variety of filtering options. You can filter by Chromosome and position, or you can use the “Other” filter to filter on any other column in the table by selecting the column from the drop down menu, choosing a sign (>=, <=, or =) and entering a value to filter on. Click “Filter” to activate all of the filters. You can then reset the filters using the reset button on the bottom right of the panel. If you have a separate dataset that shares markers with the dataset that you have already loaded, you can load it in side by side using the “Load Additional Results” button on the bottom left of the panel. Haploview can load in any results file with a single column labeled "SNP" as long as the all of the results in the column correspond to SNPs contained in the supplied map file.
In addition to viewing your results, Haploview can also go directly to the HapMap website and download the region containing the result that you specify by clicking the “Go to Selected Region” button on the bottom of the window. When you click the button, a dialog will popup to let you specify a release version of the HapMap (16a or 21), a population, and the range in kilobases that you would like to view. Click “GO” and Haploview will automatically fetch the specified region from the HapMap and load it in for LD, haplotype, and tagging analysis. Once you have loaded a region from the HapMap, the marker that you have loaded will be highlighted in blue on both the LD Plot and in the PLINK tab, which you can return to and view more results.