Before performing the meta-analysis, we applied a set of filters to each GWA results set independently. First, we removed insertions and deletions, ensuring that all base pair positions were unique and referred to the same genetic variant (that is, SNP). Second, we removed genotyped SNPs that were not in Hardy–Weinberg equilibrium (P⩽10−5). Third, we removed SNPs with minor allele frequency (MAF) <√(5/N), which under the assumption of Hardy–Weinberg equilibrium corresponded to less than five estimated individuals in the least frequent genotype group. In the EGCUT1 sample, due to very low prevalence of lifetime cannabis use (1.3%), we excluded SNPs with MAF<0.2. Fourth, regardless of the quality score type used, we excluded SNPs with imputation quality scores below 0.6. Finally, SNPs present in only one sample and SNPs with alleles or allele frequencies inconsistent with the 1000 Genomes phase I European reference panel (absolute MAF difference >0.15) were removed.
