Hi Cynthia,

I've been having the same problem with plink lately! I think if you can't get plink to work, you can remove the duplicates from the bim file yourself by writing another script in bash or python.

Here are some bash scripts I've used lately to check for dupes:

sort -u your-file.bim > duplicates-removed.bim

If you don't want it sorted for whatever reason, you can use something like this to find specific duplicate snps to remove

cat your-file.bim | cut -f1 | sort | uniq -c | sort -k2 | less -S #change f1 to index of rsID col

In the plink documentation they also have another work around for removing duplicates, here it is

grep -v '^#' reference.vcf | cut -f 3 | sort | uniq -d > reference.dups
plink --bfile reference --exclude reference.dups --make-bed --out reference

Hope any of this helps!

-BF