Plotting phenotype vs allele

Question

[MiauMiau]

Hi everyone!

I am trying to have a closer look at my, maybe, somehow weird results for which I would like to plot my quantitative phenotype against their biallelic allele distribution (i.e., box-plot with phenotype on y and allele (0, 1, 2) on x). Thus, I need to extract my SNPs of interest from the original genetic data (bed, bim, fam), further extract and match those with the IIDs from my phenotypic data, and then plot.

I tried filtering my genetic data with plink for the SNPs but it wouldn't do the same for the IIDs. I'm a little lost in how to extract the needed data correctly and then ascertain homozygous (e.g., AA, CC) or heterozygous (e.g., AC).

If anyone could point me in the right direction, I'd be very grateful! :)