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Output Files

The pVACfuse pipeline will write its results in separate folders depending on which prediction algorithms were chosen:

  • MHC_Class_I: for MHC class I prediction algorithms
  • MHC_Class_II: for MHC class II prediction algorithms
  • combined: If both MHC class I and MHC class II prediction algorithms were run, this folder combines the neoeptiope predictions from both

Each folder will contain the same list of output files (listed in the order created):

File Name Description
<sample_name>.tsv An intermediate file with variant and transcript information parsed from the input file.
<sample_name>.tsv_<chunks> (multiple) The above file but split into smaller chunks for easier processing with IEDB.
<sample_name>.all_epitopes.tsv A list of all predicted epitopes and their binding affinity scores, with additional variant information from the <sample_name>.tsv.
<sample_name>.filtered.tsv The above file after applying all filters.
<sample_name>.filtered.condensed.ranked.tsv A condensed version of the filtered TSV with only the most important columns remaining, with a priority score for each neoepitope candidate added.

Final Report Columns

In order to keep the outputs consistent, pVACfuse uses the same output columns as pVACseq but some of the values will be NA if a column doesn’t apply to pVACfuse.

Column Name Description
Chromosome The chromosome of the 5p and 3p portion of the fusion, separated by ” / “
Start The start position of the 5p and 3p portion of the fusion, separated by ” / “
Stop The stop position of the 5p and 3p portion of the fusion, separated by ” / “
Reference fusion
Variant fusion
Transcript The Ensembl IDs of the affected transcripts
Transcript Support Level NA
Ensembl Gene ID NA
Variant Type The type of fusion. inframe_fusion for inframe fusions, frameshift_fusion for frameshift fusions
Mutation NA
Protein Position The position of the fusion in the fusion protein sequence
Gene Name The Ensembl gene names of the affected genes
HLA Allele The HLA allele for this prediction
Peptide Length The peptide length of the epitope
Sub-peptide Position The one-based position of the epitope in the protein sequence used to make the prediction
Mutation Position NA
MT Epitope Seq Mutant epitope sequence
WT Epitope Seq NA
Best MT Score Method Prediction algorithm with the lowest mutant ic50 binding affinity for this epitope
Best MT Score Lowest ic50 binding affinity of all prediction algorithms used
Corresponding WT Score NA
Corresponding Fold Change NA
Tumor DNA Depth NA
Tumor DNA Depth NA
Tumor DNA Depth NA
Gene Expression NA
Transcript Expression NA
Median MT Score Median ic50 binding affinity of the mutant epitope of all prediction algorithms used
Median WT Score NA
Median Fold Change NA
Individual Prediction Algorithm WT and MT Scores (multiple) ic50 scores for the MT Epitope Seq and WT Epitope Seq for the individual prediction algorithms used
Best Cleavage Position (optional) Position of the highest predicted cleavage score
Best Cleavage Score (optional) Highest predicted cleavage score
Cleavage Sites (optional) List of all cleavage positions and their cleavage score
Predicted Stability Half Life (optional) The stability half life of the MT Epitope Seq
Stability Rank (optional) The % rank stability of the MT Epitope Seq
NetMHCstab allele (optional) Nearest neighbor to the HLA Allele. Used for NetMHCstab prediction