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This paper has investigated the sampling frequency error impact on the signal processing in a software-correlator based GPS receiver as well as the periodic averaging technique in a pre-correlation GPS signal quality monitor. The refined signal model of receiver processing in the presence of clock error is established as the foundation of the performance analyses. A software-based method is developed to accurately calibrate both the digital IF and the sampling frequency simultaneously. The method requires no additional hardware other than the GPS receiver RF front end output samples. It enables inline calibration of the receiver measurements instead of complicated post-processing. The performance of the technique is evaluated using simulated signals as well as live GPS signals collected by several GPS data acquisition equipments, including clear time domain waveforms/eye patterns, amplitude probability density histograms, Power Spectrum Density (PSD) envelopes, and correlation-related characteristics. The results show that we can calibrate the sampling frequency with an accuracy resolution of 10−9 of the true sampling frequency online, and the pre-correlation SNR can be potentially improved by 39dB using periodic averaging.