I have a dataset of chip genotypes on .bed/.bim/.fam format and I'm trying to determine if allele2 is major or ref. As of yet I do not have a confirmation about which ref build was used (but it likely is hg19).
How can I determine if a2 is major or ref? I've looked through the plink2 docs and one idea I had was to calculate a2 frequency, if it is always >0.5 then it is major. However, I can't find a proper command that calculates a2 freq, the only thing I see is reffreq which I don't understand how plink can calculate when it usually uses minor/major as a1/a2 and there is no header in plink files pointing to a reference.
But if reffreq does calc a2 freq then I guess this command would help
plink2 --bfile <prefix> --freq 'cols='reffreq
This does indeed give me a plink2.afreq file with frequencies in 2nd column, and it looks like they are all >0.5.
Is this a correct approach? Or how would I otherwise determine if a2 is major or ref?
Thanks.
