I have a set of data in PLINK format (*.bed, *.bim and *.fam files). There are around 2000 individuals in my dataset.
I used PLINK to calculate allele frequencies in the population:
p-link --bfile data --freq
However, in the produced results file, many SNPs have a MAF over 0.5 (up to 0.82). Would that not then make that the major allele frequency, as the other allele would have a frequency of 0.18?