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I am using robot_pose_ekf but am going to use a similar implementation. Does your GPS have an internal kalman filter? What NMEA message is it using? Are you using RTK? Not using these will result in large jumps in fix data. For the robot_pose_ekf, you need to set a very high covariance for some GPS data so it isn't used in the EKF, and it appears you did that as well.