A fast run for impatient users
Click here to download and install WGAViewer onto your computer.
(B) An example: loading an example dataset
Start the WGAViewer program. Click on menu “File->Open an example dataset”. Select "post-annotation dataset", and then select "CHAVI_SETPOINT_SCIENCE.wga" (Figure 3.1-1). Follow the instructions on the "Top hits" panel.
Figure 3.1-1 Load example dataset. (Click to enlarge)
(C) Real-world data: loading your dataset generated from PLINK (or other software with similar flat-text outputs)
WGAViewer supports the outputs from PLINK (Purcell et al. 2007) . To open PLINK output, click on menu “File->Open external data file->Open PLINK output”. These processes will generate and save a “.wr” input file for WGAViewer.
Figure 3.2.1-1 shows an example of the configuration of this process. In this example we load a WGA result set generated by linear regression analysis from PLINK.
 The external data set to be loaded should be separated by either space or tab key.
 It should have one row of header line indicating each column name, and at least one column for SNP and one column for P value (as shown from Figure 3.2.1-1).
 Every data row should have the same number of columns with the header row, otherwise the program will throw an error message.
 A standard MAP file (or PLINK BIM file) is also required. A MAP file has no header line, and has four columns: chromosome, SNP, genetic distance (could be 0, will not be used), and physical chromosomal location (could be from older genome build, will be annotated later).
Figure 3.2.1-1 Load external data file (Click to enlarge)
(D) Annotating your loaded dataset
Click on menu "Tool -> Top hits" to annotate the SNPs with the lowest P values. Follow the instructions, or, for details see here.