Hello. I am trying to extract data from .bed file using the following command:
./plink_linux_i686_20200616/plink --bed study.bed --bim study.bim --fam study.fam --keep-fam ii.txt --make-bed --out ii
It works for affected samples, but when I try to do the same for controls it says that there are 0 samples left after filtration. Could it be because the order of control samples is different in --keep-fam txt file and fam file itself? The order of affected samples and samples in txt file matches.