pVACseq

pVACseq is a cancer immunotherapy pipeline for the identification of personalized Variant Antigens by Cancer Sequencing (pVACseq) that integrates tumor mutation and expression data (DNA- and RNA-Seq). It enables cancer immunotherapy research by using massively parallel sequence data to predict tumor-specific mutant peptides (neoantigens) that can elicit anti-tumor T cell immunity. It is being used in studies of checkpoint therapy response and to identify targets for personalized cancer vaccines and adoptive T cell therapies. For more general information, see the manuscript published in Cancer Immunology Research.

• Features
• Input File Preparation
  • Adding genotype sample information to your VCF
  • Annotating your VCF with VEP
  • Adding coverage data to your VCF
  • Adding expression data to your VCF
  • Creating a phased VCF of proximal variants
• Getting Started
  • Running pVACseq using Docker
• Usage
• Output Files
  • Filters applied to the filtered.tsv file
  • all_epitopes.tsv and filtered.tsv Report Columns
  • all_epitopes.aggregated.tsv Report Columns
  • <sample_name>.MHC_I.all_epitopes.aggregated.ML_predict.tsv Report Columns
  • aggregated.tsv.reference_matches Report Columns
• Filtering Commands
  • Binding Filter
  • Coverage Filter
  • Transcript Filter
  • Top Score Filter
  • Aggregate Report Filter
• Additional Commands
  • Download Example Data
  • Install VEP Plugin
• Optional Downstream Analysis Tools
  • Generate Protein Fasta
  • Generate Aggregated Report
  • Add Evaluation Predictions Using a Pre-Trained Machine Learning Model
  • Calculate Reference Proteome Similarity
  • NetChop Predict Cleavage Sites
  • NetMHCStab Predict Stability
  • Identify Problematic Amino Acids
  • Mark Genes of Interest
  • Update Tiers
  • Create Peptide Ordering Form
• Common Errors
  • Input VCF Sample Information
  • Input VCF Compression and Indexing
  • Input VCF VEP Annotation
  • Other
• Frequently Asked Questions