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For a single-cohort based GWAS, the GWAS cohort itself can be used as the reference set. For a meta-analysis, you can use one of the largest participating cohorts as the reference set. If none of them are available, you might use data from the 1000 Genomes Project (you will need PLINK2 --vcf option to convert the data into PLINK binary PED format).
Please see Figure 1 of Bakshi et al.