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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?

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  • $\begingroup$ 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
    Commented Jan 11, 2017 at 15:17
  • $\begingroup$ You should post an example section from your data file that reports MAF>0.5. $\endgroup$
    – WYSIWYG
    Commented Mar 12, 2019 at 16:16

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