If I can figure out the software, I should be able to do the rest on my own. What I really like is overlaying the LD matrix with the association p-value vs chromosomal position plot. Therefore, I would also be interested in other packages that do this.
Lastly, if anyone has code to do this, I would be very thankful, but my first priority is just to find software options.
Edit: searching on my own revealed snp.plotter R package as the likely source of this, can anyone confirm that? Another package that might work for me is the locuszoom standalone. Are there other options I should know about?