I am following this tutorial on running GWAS analyses:
Basic statistical analysis in genetic case-control studies
(you will need probably academic access to Nature so you don't have to buy the article).
I used the gwas data found at http://www.well.ox.ac.uk/ggeu/NPanalysis/ and followed the instructions dutifully.
When I go to plot the Manhattan plot, however, I get a Java GC limit error. Specifically the error message reads:
Fatal Error: Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: GC overhead limit exceeded
I can't tell if this is a Java error, or a Haploview error. I added the following Java parameter when I launched Haploview, to increase the max heap size allocated to Haploview, but it did not help.
java -jar -Xmx2048M Haploview.jar