Can/why can gPLINK perform a particular PLINK command?
gPLINK is intended only as a lightweight interface to some of the basic PLINK commands. It is designed to provide an easy way to become familiar with PLINK and to perform certain very basic operations for users who are not yet familiar with command line interfaces. It is not the recommended mode for using PLINK for anything beyond the most basic analyses and there are no immediate plans to extend gPLINK any further to incorporate new commands that are added to PLINK.