Methods and systems for instrument tracking and navigation are described. In one embodiment, the system may be configured to receive position sensor data from at least one position sensor tracking an instrument positioned within a luminal network and determine a position sensor-based estimated state derived from the sensor data. The system may be configured to determine a combined estimated state for the instrument based on the position sensor data and at least one other type of position data. The system may be configured to determine a location transform based on the combined estimated state and the position sensor-based estimated state and output an estimated state of the instrument based on the position sensor-based estimated state adjusted by the location transform.
