Merge beds of same cohorts: one from chip and one from exome data

Question

[njbernstein]

Hi all,

I have two bed files each representing similar cohorts (a few subjects are not in the other). I'm trying to merge the files there is a concatenation of sorts of the calls of the same subject from both cohorts without duplication (when there is duplication always relying on the chip genotypes).

I know plink has a merge function, but best I can tell it only merges based on calls, and I'd like to merge based on subjects, i.e. combining the calls from the two platforms into one file with each subject only being represented once. Any help would be much appreciated.

Best