pVACfuse

This component of the pVACtools workflow provides support for predicting neoantigens from gene fusions. Currently, annotated fusion variants as reported by AGFusion and Arriba are supported, and any of the binding affinity prediction software available in pVACseq can be used for binding prediction.

• Features
• Prerequisites
  • Fusion detection and annotation using AGFusion
  • Fusion detection and annotation using Arriba
  • Running STAR-Fusion for read support and expression information
• Getting Started
• Usage
• Output Files
  • Filters applied to the filtered.tsv file
    • Prediction Algorithms Supporting Presentation Scores
    • Prediction Algorithms Supporting Immunogenicity Scores
    • Prediction Algorithms Supporting Percentile Information
  • all_epitopes.tsv and filtered.tsv Report Columns
  • all_epitopes.aggregated.tsv Report Columns
    • The pVACfuse Aggregate Report Tiers
      • Tiering Parameters
      • Tiers
      • Criteria Details
    • The pVACfuse Aggregate Report Sorting
  • aggregated.tsv.reference_matches Report Columns
• Filtering Commands
  • Binding Filter
  • Coverage Filter
  • Top Score Filter
• Additional Commands
  • Download Example Data
  • List Valid Alleles
  • List Valid Algorithms
  • List Valid NetMHCIIpan/NetMHCIIpanEL Versions
  • List Allele-Specific Cutoffs
• Optional Downstream Analysis Tools
  • Generate Protein Fasta
  • Generate Aggregated Report
  • Calculate Reference Proteome Similarity
  • NetChop Predict Cleavage Sites
  • NetMHCStab Predict Stability
  • Identify Problematic Amino Acids
  • Mark Genes of Interest
  • Update Tiers