I am trying to solve a problem with my genotyped array data set. For reason or another, the data set has duplicate or with three different names pointing to the same position. For example:
I want to build a list for SNP names to be removed (so I can exclude them in PLINK).
So from the SNPs above, snp_1 or snp_3 and snp_2 should be in removal list.
How would I achieve this?