pVACfuse

This component of the pVACtools workflow provides support for predicting neoantigens from gene fusions. Currently, fusion variants as reported by INTEGRATE-Neo 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
• Getting Started
• Usage
• Output Files
  • Filters applied to the filtered.tsv file
    • Prediction Algorithms Supporting Percentile Information
  • all_epitopes.tsv and filtered.tsv Report Columns
  • filtered.tsv.reference_matches Report Columns
  • all_epitopes.aggregated.tsv Report Columns
• Filtering Commands
  • Binding Filter
  • Top Score Filter
• Additional Commands
  • Download Example Data
  • List Valid Alleles
  • 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