A python script to remove duplicate snps from plink files and recode the resultant files into plink binaries free of duplicate snps plink needs to be installed and in shell path, A .tped file needs to be given to the script you can generate a .tped file by plink --bfile XXX --recode transpose XXX will match on the chr:pos so multi-alleleic variants will be explicitly filtered keeping the first instance
python removeDup.py -T your_tpedfile.tped