Run PX4 without Commander

I am interested in using px4 just to get EKF solution. Is it possible to run it without the commander module?
The current setup is to attach a Pixhawk to the drone and just extract the position data. Since we never use the Pixhawk for navigation it stays in standby mode and commander never stops preflight checks. Is it possible to run just ekf2 module without the commander module? Or is it possible to change the vehicle status from STANDBY to ARMED manually?