The performance of GNSS based positioning services is improving to the benefit of the users, and the uncertainties from densified RTK networks for construction work is approaching the sub-centimeter level also in the vertical. The error sources related to the continuously operating reference stations (CORS) may therefore soon be limiting factors for further improvement of performance. Station dependent effects are thus important in high accuracy GNSS positioning. Electrical coupling between the antenna and its near-field environment changes the characteristics of the antenna from what has been determined in e.g. absolute robot or chamber calibrations. Since the first initial tests back in 2008, Lantmäteriet together with Chalmers University of Technology and Research Institute of Sweden (RISE), has carried out in-situ station calibration of its network of permanent reference stations, SWEPOS. The station calibration intends to determine the electrical center of the GNSS antenna, as well as the PCV (phase center variations) when the antenna is installed at a SWEPOS station. One purpose of the calibration is to examine the site-dependent effects on the height determination in SWEREF 99 (the national reference frame). Another purpose is to establish PCV as a complement to absolute calibrations of the antenna-radome pair. In this paper we present both the methodology for observation procedure in the field and the method for the analysis, together with results of the station-dependent effects on heights as well as PCV from the analysis. Some strength and weakness of our method for GNSS station calibration are discussed at the end.