You can do that with nvvidconv (here cropping a 800x600 ROI starting at x=150 and y=100:
nvarguscamerasrc ! video/x-raw(memory:NVMM), width=1280, height=720, format=NV12, framerate=20/1 ! nvvidconv left=150 right=949 top=100 bottom=699 ! video/x-raw, width=800, height=600, format=BGRx ! videoconvert ! video/x-raw,format=BGR ! appsink drop=1