In the past, the analysis of JET polarimetry measurements were carried out only for the vertical channels using a polarimetry propagation code based on the Stokes vector formalism. A new propagation code has been developed therefore for the lateral chords to simulate and interpret the measurements of the Faraday rotation and Cotton-Mouton phase shift in JET. The code has been used to develop a theoretical study to the effect of the input polarization on the eventual quality of the measurements. The results allow choosing the best polarization to optimize the polarimetric measurements for the various experiments.