This is a promising alternative showing through RCN3/FCGRN with gwas2.sh.
graph TB;
gwas2.sh --> gwas.do
gwas2.sh --> gwas2.do
where gwas.do (caprion.dat also contains _invn data) and gwas2.do (gwas2_invn.do for _invn data) are for the pilot and batch 2 data, respectively.
See gwas2 repository for additional information.