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?

  • $\begingroup$ can you add some more info about PLINK format and background info for the question so other users not as familiar can follow? $\endgroup$ – Vance L Albaugh Jan 11 '17 at 15:17
  • $\begingroup$ You should post an example section from your data file that reports MAF>0.5. $\endgroup$ – WYSIWYG Mar 12 '19 at 16:16