Hello,

Is there a way to combine two separate sets of bfiles (.bed, .bim and .fam in each set), so that all of the individuals are in a one set of files?

If you have common set of SNPs between your two set of bfiles (PLINK files), you can use plink --bmerge command to merge them as follows:

plink --bfile first_data --bmerge second_data.bed second_data.bim second_data.fam --allow-no-sex --make-bed --out merged_data