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Output Files

The pVACbind 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



An intermediate file with variant information parsed from the input files.

<sample_name>.tsv_<chunks> (multiple)

The above file but split into smaller chunks for easier processing with IEDB.


A list of all predicted epitopes and their binding affinity scores, with additional variant information from the <sample_name>.tsv.


The above file after applying all filters, with cleavage site and stability predictions added.

Filters applied to the filtered.tsv file

The filtered.tsv file is the all_epitopes file with the following filters applied (in order):

  • Binding Filter

  • Top Score Filter

Please see the Standalone Filter Commands documentation for more information on each individual filter. The standalone filter commands may be useful to reproduce the filtering or to chose different filtering thresholds.

all_epitopes.tsv and filtered.tsv Report Columns

Column Name



The FASTA ID of the peptide sequence the epitope belongs to

HLA Allele

The HLA allele for this prediction

Sub-peptide Position

The one-based position of the epitope in the protein sequence used to make the prediction

Epitope Seq

The epitope sequence

Median Score

Median ic50 binding affinity of the epitope of all prediction algorithms used

Best Score

Lowest ic50 binding affinity of all prediction algorithms used

Best Score Method

Prediction algorithm with the lowest ic50 binding affinity for this epitope

Individual Prediction Algorithm Scores (multiple)

ic50 scores for the Epitope Seq for the individual prediction algorithms used


Mean hydropathy of last 7 residues on the C-terminus of the peptide


Max GRAVY score of any kmer in the amino acid sequence. Used to determine if there are any extremely hydrophobic regions within a longer amino acid sequence.

difficult_n_terminal_residue (T/F)

Is N-terminal amino acid a Glutamine, Glutamic acid, or Cysteine?

c_terminal_cysteine (T/F)

Is the C-terminal amino acid a Cysteine?

c_terminal_proline (T/F)

Is the C-terminal amino acid a Proline?


Number of Cysteines in the amino acid sequence. Problematic because they can form disulfide bonds across distant parts of the peptide

n_terminal_asparagine (T/F)

Is the N-terminal amino acid a Asparagine?


Number of Asparagine-Proline bonds. Problematic because they can spontaneously cleave the peptide

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 (optional)

Stability of the pMHC-I complex

Half Life (optional)

Half-life of the pMHC-I complex

Stability Rank (optional)

The % rank stability of the pMHC-I complex

NetMHCstab allele (optional)

Nearest neighbor to the HLA Allele. Used for NetMHCstab prediction