A major challenge in the development of peptide-based vaccines is finding the right immunogenic element, with efficient and long-lasting immunisation effects, from large potential targets encoded by pathogen genomes. Computer models are convenient tools for scanning pathogen genomes to pre-select candidate immunogenic peptides for experimental validation. Current methods predict many false positives resulting from a low prevalence of true positives. We develop a test reject method based on the prediction uncertainty estimates determined by Gaussian process regression. This method filters false positives amongst predicted epitopes from a pathogen genome. The performance of stand-alone Gaussian process regression is compared to other state-of-the-art methods using cross-validation on eleven benchmark data sets. The results show that the Gaussian process method has the same accuracy as the top performing algorithms. The combination of Gaussian process regression with the proposed test reject method is used to detect true epitopes from the Vaccinia virus genome. The test rejection increases the prediction accuracy by reducing the number of false positives without sacrificing the method's sensitivity. We show that the Gaussian process in combination with test rejection is an effective method for prediction of T-cell epitopes in large and diverse pathogen genomes, where false positives are of concern.