Various population genetics analyses have a requirement that the provided genotypes are only of unlinked markers. This can be easily accomplished with PLINK using the --indep-pairwise flag.
When working with different populations, should one remove the linked markers per population, and then merge subsequently (losing any markers not shared), or can one merge all the populations and then filter for linked markers? Intuitively, it seems that merging beforehand might mask the effects of linkage within the populations.
PS. I guess this isn't a PLINK (or SNP) specific question, but I'm using it as the example