How to calculate average minor allele frequency (MAF) difference between two populations (i.e. European, Hispanic) The data is present in the PLINK format .bed (individual genotypes), .bim (genetic markers) and .fam (sample IDs and disease phenotype file). I have also separate text files containing information on subjects related to two populations. (i.e. European and Hispanic)
You need to report allele frequencies using plink for some European samples
Do the same for Hispanic samples
Use a software to subtract the two allele frequencies obtained above and obtain the result.