due to data protection constraints I have to permute my patient data in the .ped-file (while keeping the SNPs and the ordering of the SNPs unchanged) before sending the data to my collaboration partner. I didn't change the .map file.
Now I generated the .bim/.bed/.fam-files using PLINK out of the original data set and the permuted data set to check whether the results differ. Unfortunately, the.bim-files have some entries where allel 1 and 2 are ordered differently meaning that allel 1 became allel 2 and vice versa. I am not a Bioinformatic person and so my question is: Does this matter? Why is the order of the patients important for the definition of allel 1/2?
Thanks in advance!