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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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closed as unclear what you're asking by AliceD Mar 25 at 8:17

Please clarify your specific problem or add additional details to highlight exactly what you need. As it's currently written, it’s hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

  • $\begingroup$ 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 at 16:16