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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

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

File Name Description
log A log file of the parameters used for this run
<sample_name>.tsv An intermediate file with variant, transcript, coverage, vaf, and expression information parsed from the input files.
<sample_name>.tsv_<chunks> (multiple) The above file but split into smaller chunks for easier processing with IEDB.
<sample_name>.combined.parsed.tsv A modified version of the <sample_name>.tsv file with binding scores from IEDB added.
<sample_name>.filtered.binding.tsv The above file after filtering by binding threshold.
<sample_name>.filtered.top.tsv (optional) The above file after picking the top epitope for each variant (optional).
<sample_name>.chop.tsv (optional) The above file with cleavage site predictions added (optional).
<sample_name>.stab.tsv (optional) The above file with stability predictions added (optional).
<sample_name>.final.tsv (optional) The final output file after all filtering and optional steps.

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
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 Eptiope 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