Dear Dr Atkinson,
Thank you for providing the code to execute LAI prior to Tractor.
When exectuing the CohortDataQC_final.sh script I've this error :
python: can't open file 'update_rsID_bim_ega.py': [Errno 2] No such file or directory
In the files listed on the github there is no update_rsID_bim_ega.py file. There is update_rsID_bim_arg.py instead.
Also it seems to be python2 and not python3.
After updating the path to the python script in CohortDataQC_final.sh and forcing the script to use python2, the script is now working well ;)