I use an Electroharmonix Pitch Fork pedal to do the same thing and it works just fine going straight from guitar to pedal to computer. It is similar to the Drop pedal, but can also shift the pitch up, and has a dial for preset intervals like M3, P4, P5, 1-3 Octaves etc. My only gripe is that it doesn't have a minor 3rd setting so I can't easily go from E standard to C# standard...