Volkswagen specifically states that putting biodiesel in your tank will void your warranty and many people have had their vehicles fail. Unfortunately B10 or B20 (10% or 20% biodiesel) is all that's available in several midwestern states.
Be forewarned -- filling your VW up with diesel can kill it.
Put a fuel pump in the thing that can deal with biodiesel. With biodiesel being mandated in several states now, the fact that VW continues selling the TDI into states where driving it off the dealer lot and putting diesel fuel into it voids the warranty is a consumer nightmare that VW needs to address rather than using the Sgt. Schultz defense ("I see no-think! I hear no-think!").