pVACtools 3.1.1 documentation
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Table of Contents

  • pVACseq
  • pVACbind
  • pVACfuse
    • Features
    • Prerequisites
    • Getting Started
    • Usage
    • Output Files
    • Filtering Commands
    • Additional Commands
    • Optional Downstream Analysis Tools
  • pVACvector
  • pVACview
  • Installation
  • Tools Used By pVACtools
  • Frequently Asked Questions
  • Release Notes
  • License
  • Citations
  • How To Contribute
  • Contact
  • Mailing List

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pVACfuse logo

pVACfuseΒΆ

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
  • pVACtools 3.1.1 documentation
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