Here is most of the code I used to produce my LocusFocus results. It is missing the part used to run PoPs but that fairly straightforward and I followed the instructions on their GitHub Repo.
Analyses were done with python or R, in the scripts. Ignore the Jupyter notebook as that was from very early on.
If there are any problems or issues with the code feel free to contact me obba2@cam.ac.uk. Also to see the most up-to date version of this repo on my personal Github.