I am trying to recode alleles for my .bim file in PLINK , for example from A,B allele coding to A,C,G,T.
1 rs101 0 4566795 A B
1 rs102 0 4640902 B A
PLINK requires that you use the --update-alleles command ./plink --bfile mydata --update-alleles mylist.txt --make-bed --out newfile with which the file mylist.txt contains five columns per row listing For example,
rs101 A B G T rs102 A B A C
My question is when creating the "mylist.txt" file, for the last two columns, How do you determine the new allele code for first allele and the new allele code for other allele ( A is no G, B is now T)?