How to read rotary encoder with VF50?

How to use the rotary encoder channel pins 28 & 67 to read the rotary encoder with VF50?

What OS and which version thereof are you targeting?

Connect Phase A and Phase B signals from your rotary encoder to pins 28 and 67. Set up pin mux properly and program FTMx_QDCTRL register according to your encoder spec. Then you can read rotation counter from FTM register.
See the Quadrature Decoder mode section at the VFxxx Controller Reference Manual for more details.

Colibri VF50, Iris V1.0 carrier board, Wince6

pin 28 and 67 are available as PWM output pins on the toradex carrier board. Can you please explain the procedure so that I can get the reading in my application?