Phonon dispersion relations and electron-phonon coupling of hole-doped trigonal GeTe have been computed by density functional perturbation theory. This compound is a prototypical phase change material of interest for applications in phase change non-volatile memories. The calculations allowed us to estimate the electron-phonon contribution to the thermal boundary resistance at the interface between the crystalline and amorphous phases present in the device. The lattice contribution to the thermal boundary resistance has been computed by non-equilibrium molecular dynamics simulations with an interatomic potential based on a neural network scheme. We find that the electron-phonon term contributes to the thermal boundary resistance to an extent which is strongly dependent on the concentration and mobility of the holes. Further, for measured values of the holes concentration and electrical conductivity, the electron-phonon term is larger than the contribution from the lattice. It is also shown that the presence of Ge vacancies, responsible for the p-type degenerate character of the semiconductor, strongly affects the lattice thermal conductivity of the crystal.