Define parameters to run the mutect paired algorithm.

def cl_mutect(self, params, tmp_dir):
        """Define parameters to run the mutect paired algorithm.
        """
        gatk_jar = self._get_jar("muTect", ["mutect"])
        # Decrease memory slightly from configuration to avoid memory allocation errors
        jvm_opts = config_utils.adjust_opts(self._jvm_opts,
                                            {"algorithm": {"memory_adjust":
                                                           {"magnitude": 1.1, "direction": "decrease"}}})
        return ["java"] + jvm_opts + get_default_jvm_opts(tmp_dir) + \
               ["-jar", gatk_jar] + [str(x) for x in params]