Output Files

The pVACseq 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.coverage.tsv (optional)	The above file after filtering on coverage, VAF, and expression values (optional).
<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

Column Name	Description
Chromosome	The chromosome of this variant
Start	The start position of this variant in the zero-based, half-open coordinate system
Stop	The stop position of this variant in the zero-based, half-open coordinate system
Reference	The reference allele
Variant	The alt allele
Transcript	The Ensembl ID of the affected transcript
Ensembl Gene ID	The Ensembl ID of the affected gene
Variant Type	The type of variant. missense for missense mutations, inframe_ins for inframe insertions, inframe_del for inframe deletions, and FS for frameshift variants
Mutation	The amnio acid change of this mutation
Protein Position	The protein position of the mutation
Gene Name	The Ensembl gene name of the affected gene
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	The one-based position of the start of the mutation in the epitope. 0 if the start of the mutation is before the epitope
MT Epitope Seq	Mutant epitope sequence
WT Epitope Seq	Wildtype (reference) epitope sequence at the same position in the full protein sequence. NA if there is no wildtype sequence at this position or if more than half of the amino acids of the mutant epitope are mutated
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	ic50 binding affinity of the wildtype epitope. NA if there is no WT Epitope Seq.
Corresponding Fold Change	Corresponding WT Score / Best MT Score. NA if there is no WT Epitope Seq.
Tumor DNA Depth	Tumor DNA depth at this position. NA if no bam-readcount file provided.
Tumor DNA VAF	Tumor DNA variant allele frequency at this position. NA if no bam-readcount file provided.
Tumor DNA Depth	Tumor RNA depth at this position. NA if no bam-readcount file provided.
Tumor DNA VAF	Tumor RNA variant allele frequency at this position. NA if no bam-readcount file provided.
Tumor DNA Depth	Normal DNA depth at this position. NA if no bam-readcount file provided.
Tumor DNA VAF	Normal DNA variant allele frequency at this position. NA if no bam-readcount file provided.
Gene Expression	Gene expression value at this position. NA if no cufflinks file provided.
Transcript Expression	Transcript expression value at this position. NA if no cufflinks file provided.
Median MT Score	Median ic50 binding affinity of the mutant epitope of all prediction algorithms used
Median WT Score	Median ic50 binding affinity of the wildtype epitope of all prediction algorithms used. NA if there is no WT Epitope Seq.
Median Fold Change	Median WT Score / Median MT Score. NA if there is no WT Epitope Seq.
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