Workflow for in silico mapping of the somatic landscape of tumors to putative immunogenic neoantigens for clinical applications. Blue text indicates steps that are less commonly performed. References for further reading are included in parentheses. Abbreviations: aa, amino acids; HLA, human leukocyte antigen; LOH, loss of heterozygosity; MHC, major histocompatibility complex; MHC-I, MHC class I; MHC-II, MHC class II; uORF, upstream open reading frame.