Hi, you may want to contact Auvidea, they were using CAN bus on their carriers in communication with AutoQuad autopilot.
Other autopilots I know of having been integrated with Jetson use a serial connection or MAVlink as opposed to CAN bus. See this ArduPilot guide or NVIDIA Redtail project to setting up Pixhawk or APM with Jetson.
The DJI Matrice platform also enables connecting it’s flight controller to Jetson, see this related post from JetsonHacks.