pVACsplice

pVACsplice predicts neoantigens for novel junctions created from tumor-specific alternative splicing patterns.

• Features
• Input File Preparation
  • Step 1: Annotate VCF file
  • Step 2: Run RegTools
• Getting Started
• Usage
• Output Files
  • Filters applied to the filtered.tsv file
    • Prediction Algorithms Supporting Percentile Information
    • Prediction Algorithms Supporting Presentation Scores
    • Prediction Algorithms Supporting Immunogenicity Scores
  • all_epitopes.tsv and filtered.tsv Report Columns
  • all_epitopes.aggregated.tsv Report Columns
    • Best Peptide Criteria
    • The pVACsplice Aggregate Report Tiers
      • Tiering Parameters
      • Tiers
      • Criteria Details
    • The pVACsplice Aggregate Report Sorting
  • aggregated.tsv.reference_matches Report Columns
• Filtering Commands
  • Binding Filter
  • Coverage Filter
  • Transcript Filter
  • Top Score Filter
• Additional Commands
  • Download Example Data
  • List Valid Alleles
  • 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