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neoantigen-prediction

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Identify tumor neoantigens from somatic variants with pVACtools (pVACseq/pVACfuse/pVACbind/pVACvector/pVACview) for personalized cancer vaccines and checkpoint biomarkers. Encodes the field's hard truth that binding prediction is the easy, near-solved part and single-digit-percent PPV lives downstream — so it centers clonality/CCF, HLA LOH (the silent invalidator), expression, proximal-variant phasing, agretopicity/foreignness quality, and the predicted->presented->immunogenic validation tiers. Use when nominating vaccine targets, ranking neoantigens, or building a tumor-to-candidate pipeline. Binding details in mhc-binding-prediction; ranking in immunogenicity-scoring.

When to use

• nominating vaccine targets
• ranking neoantigens
• building a tumor-to-candidate pipeline
• identifying tumor neoantigens from somatic variants
• predicting patient-HLA presentation
• processing fusion-junction novel-ORF neoantigens
• scoring arbitrary peptides
• ordering epitopes into a vaccine string

When not to use

• binding details
• ranking in immunogenicity-scoring

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