We present and compare different numerical schemes for the integration of the variational equations of autonomous Hamiltonian systems whose kinetic energy is quadratic in the generalized momenta and whose potential is a function of the generalized positions. We apply these techniques to Hamiltonian systems of various degrees of freedom, and investigate their efficiency in accurately reproducing well-known properties of chaos indicators like the Lyapunov Characteristic Exponents (LCEs) and the Generalized Alignment Indices (GALIs). We find that the best numerical performance is exhibited by the textit{`tangent map (TM) method}, a scheme based on symplectic integration techniques which proves to be optimal in speed and accuracy. According to this method, a symplectic integrator is used to approximate the solution of the Hamiltons equations of motion by the repeated action of a symplectic map $S$, while the corresponding tangent map $TS$, is used for the integration of the variational equations. A simple and systematic technique to construct $TS$ is also presented.
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