Output Files

The pVACsplice pipeline will write a few files to the main output directory. These files contain information about the processed splice sites that aren’t specific to either class of prediction algorithm:

• <sample_name>.transcripts.fa and matching .fai index file: A fasta file of wildtype and splice site peptide sequences for splice sites predicted by RegtTools and supported by pVACsplice.

• <sample_name>_combined.tsv: A TSV file combining information for each splice site from the RegTools TSV and the input VCF.

pVACsplice writes 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 neoepitope predictions from both

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

File Name	Description
<sample_name>.all_epitopes.tsv	A list of all predicted epitopes and their binding affinity scores, with additional variant information.
<sample_name>.filtered.tsv	The above file after applying all filters, with (optionally) cleavage site, and stability predictions added.
<sample_name>.all_epitopes.aggregated.tsv	An aggregated version of the all_epitopes.tsv file that gives information about the best epitope for each mutation in an easy-to-read format. Not generated when running with elution algorithms only.
<sample_name>.all_epitopes.aggregated.tsv.reference_matches (optional)	A file outlining details of reference proteome matches

Additionally, each folder will contain subfolders, one for each selected epitope length, that contains intermediate files that are specific to each epitope length.

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

• Coverage Filter

• Transcript Support Level 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.

Prediction Algorithms Supporting Percentile Information

pVACseq outputs binding affinity percentile rank information when provided by a chosen prediction algorithm. The following prediction algorithms calculate a percentile rank:

• MHCflurry

• NetMHC

• NetMHCcons

• NetMHCpan

• NetMHCIIpan

• NNalign

• PickPocket

• SMM

• SMMPMBEC

• SMMalign

The following prediction algorithms do not provide a percentile rank:

• MHCnuggets

Prediction Algorithms Supporting Elution Scores

• MHCflurryEL

• NetMHCpanEL

• NetMHCIIpanEL

• BigMHC_EL

Prediction Algorithms Supporting Immunogenicity Scores

• BigMHC_IM

• DeepImmuno

Please note that when running pVACseq with only elution or immunogenicity algorithms, no aggregate report and pVACview files are created.

all_epitopes.tsv and filtered.tsv 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
Junction	Junction ID in regtools output
Junction Start	The start position of this junction in the zero-based, half-open coordinate system
Junction Stop	The stop position of this junction in the zero-based, half-open coordinate system
Junction Score	The number of reads supporting the junction. (integer)
Junction Anchor	Field that specifies the donor, acceptor configuration. See Notes (D/A/DA/NDA/N)
Transcript	The Ensembl ID of the affected transcript
Transcript Support Level	The transcript support level (TSL) of the affected transcript. Not Supported if the VCF entry doesn’t contain TSL information.
Biotype	The biotype 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
Amino Acid Change	The amnio acid change of this mutation
Gene Name	The Ensembl gene name of the affected gene
HGVSc	The HGVS coding sequence variant name
HGVSp	The HGVS protein sequence variant name
WT Protein Length	Length of fully-translated wildtype protein
ALT Protein Length	Length of fully-translated alternate protein
Frameshift Event	Is the variant a frameshift event? (yes/no)
Protein Position	Starting position of Epitope (Position of the first amino acid of selected epitope in the fully-translated protein)
HLA Allele	The HLA allele for this prediction
Peptide Length	The peptide length of the epitope
Epitope Seq	The mutant epitope sequence
Median IC50 Score	Median ic50 binding affinity of the mutant epitope across all prediction algorithms used
Best IC50 Score	Lowest ic50 binding affinity of all prediction algorithms used
Best IC50 Score Method	Prediction algorithm with the lowest mutant ic50 binding affinity for this epitope
Median Percentile	Median binding affinity percentile rank of the mutant epitope across all prediction algorithms (those that provide percentile output)
Best Percentile	Lowest percentile rank of this epitope’s ic50 binding affinity of all prediction algorithms used (those that provide percentile output)
Best Percentile Method	Prediction algorithm with the lowest binding affinity percentile rank for this epitope
Tumor DNA Depth	Tumor DNA depth at this position. NA if VCF entry does not contain tumor DNA readcount annotation.
Tumor DNA VAF	Tumor DNA variant allele frequency (VAF) at this position. NA if VCF entry does not contain tumor DNA readcount annotation.
Tumor RNA Depth	Tumor RNA depth at this position. NA if VCF entry does not contain tumor RNA readcount annotation.
Tumor RNA VAF	Tumor RNA variant allele frequency (VAF) at this position. NA if VCF entry does not contain tumor RNA readcount annotation.
Normal Depth	Normal DNA depth at this position. NA if VCF entry does not contain normal DNA readcount annotation.
Normal VAF	Normal DNA variant allele frequency (VAF) at this position. NA if VCF entry does not contain normal DNA readcount annotation.
Gene Expression	Gene expression value for the annotated gene containing the variant. NA if VCF entry does not contain gene expression annotation.
Transcript Expression	Transcript expression value for the annotated transcript containing the variant. NA if VCF entry does not contain transcript expression annotation.
Index	A unique idenitifer for this variant-transcript combination
Fasta Key	the number identifier for corresponding altered peptide isoform in pvac output fasta
Individual Prediction Algorithm  IC50 Scores and Percentiles (multiple)	ic50 binding affintity and percentile ranks for the Epitope Seq for the individual prediction algorithms used
MHCflurryEL WT and MT Processing Score and Presentation Score and Percentile (optional)	MHCflurry elution processing score and presentation score and percentiles for the Epitope Seq if the run included MHCflurryEL as one of the prediction algorithms
cterm_7mer_gravy_score	Mean hydropathy of last 7 residues on the C-terminus of the peptide
max_7mer_gravy_score	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?
cysteine_count	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?
asparagine_proline_bond_count	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

all_epitopes.aggregated.tsv Report Columns

The all_epitopes.aggregated.tsv file is an aggregated version of the all_epitopes TSV. It shows the best-scoring epitope for each variant, and outputs additional binding affinity, expression, and coverage information for that epitope. It also gives information about the total number of well-scoring epitopes for each variant, the number of transcripts covered by those epitopes, as well as the HLA alleles that those epitopes are well-binding to. Lastly, the report will bin variants into tiers that offer suggestions as to the suitability of variants for use in vaccines.

Only epitopes meeting the --aggregate-inclusion-binding-threshold are included in this report (default: 5000). If the number of unique epitopes for a variant meeting this threshold exceeds the --aggregate-inclusion-count-limit, only the n best-binding epitopes up to this limit are included (default: 15). If the Best Peptide does not meet the aggregate inclusion criteria, it will be still be counted in the Num Included Peptides.

Whether the median or the lowest binding affinity metrics are used for determining the included eptiopes, selecting the best-scoring epitope, and which values are output in the IC50 MT and %ile MT columns is controlled by the --top-score-metric parameter.

Column Name	Description
ID	A unique identifier for the junction (Gene name . transcript. Junction ID . variant chr . variant start - variant stop . junction type)
HLA Alleles (multiple)	For each HLA allele in the run, the number of this variant’s epitopes that bound well to the HLA allele (with median/lowest mutant binding affinity < binding_threshold)
Gene	The Ensembl gene name of the affected gene
Transcript	The Ensembl ID of the affected transcript
Junction Name	junction ID from regtools output
AA Change	The amino acid change for the mutation
Best Peptide	The best-binding mutant epitope sequence (see Best Peptide Criteria below for more details on how this is determined)
TSL	The Transcript Support Level of the Transcript
Allele	The Allele that the Best Peptide is binding to
Pos	The one-based position of the start of the mutation within the epitope sequence. 0 if the start of the mutation is before the epitope (as can occur downstream of frameshift mutations)
Prob Pos	A list of positions in the Best Peptide that are problematic. None if the --problematic-pos parameter was not set during the pVACseq run
Num Included Peptides	The number of included peptides according to the --aggregate-inclusion-binding-threshold and --aggregate-inclusion-count-limit
Num Passing Peptides	The number of unique well-binding peptides for this mutation.
IC50 MT	Median or lowest ic50 binding affinity of the best-binding mutant epitope across all prediction algorithms used
%ile MT	Median or lowest binding affinity percentile rank of the best-binding mutant epitope across all prediction algorithms used (those that provide percentile output)
RNA Expr	Gene expression value for the annotated gene containing the variant.
RNA VAF	Tumor RNA variant allele frequency (VAF) at this position.
Allele Expr	RNA Expr * RNA VAF
RNA Depth	Tumor RNA depth at this position.
DNA VAF	Tumor DNA variant allele frequency (VAF) at this position.
Tier	A tier suggesting the suitability of variants for use in vaccines.
Ref Match (T/F) (optional)	Was there a match of the mutated peptide sequence to the reference proteome?
Evaluation	Column to store the evaluation of each variant when evaluating the run in pVACview. Either Accept, Reject, or Review.

Best Peptide Criteria

To determine the Best Peptide, all peptides meeting the --aggregate-inclusion-threshold and --aggregate-inclusion-count-limit (see above) are evaluated as follows:

• Pick the entries with no Problematic Positions.

• Of the remaining entries, pick the one with the lowest median/best MT IC50 score.

The pVACsplice Aggregate Report Tiers

Tiering Parameters

To tier the Best Peptide, several cutoffs can be adjusted using arguments provided to the pVACsplice run:

Parameter	Description	Default
--binding-threshold	The threshold used for filtering epitopes on the IC50 MT binding affinity.	500
--allele-specific-binding-thresholds	Instead of the hard cutoff set by the --binding-threshold, use allele-specific binding thresholds. For alleles where no allele-specific binding threshold is available, use the --binding-threshold as a fallback. To print a list of alleles that have specific binding thresholds and the value of those thresholds, run pvacseq allele_specific_cutoffs.	False
--percentile-threshold	When set, use this threshold to filter epitopes on the %ile MT score in addition to having to meet the binding threshold.	None
--tumor-purity	Value between 0 and 1 indicating the fraction of tumor cells in the tumor sample. Information is used for a simple estimation of whether variants are subclonal or clonal based on VAF. If not provided, purity is estimated directly from the VAFs.	None
--trna-vaf	Tumor RNA VAF Cutoff. Used to calculate the allele expression cutoff for tiering.	0.25
--trna-cov	Tumor RNA Coverage Cutoff. Used as a cutoff for tiering.	10
--expn-val	Gene and Expression cutoff. Used to calculate the allele expression cutoff for tiering.	1.0
--maximum-transcript-support-level	The threshold to use for filtering epitopes on the Ensembl transcript support level (TSL). Transcript support level needs to be <= this cutoff to be included in most tiers.	1
--allele-specific-anchors	Use allele-specific anchor positions when tiering epitopes in the aggregate report. This option is available for 8, 9, 10, and 11mers and only for HLA-A, B, and C alleles. If this option is not enabled or as a fallback for unsupported lengths and alleles, the default positions of [1, 2, epitope length - 1, and epitope length] are used. Please see https://doi.org/10.1101/2020.12.08.416271 for more details.	False
--anchor-contribution-threshold	For determining allele-specific anchors, each position is assigned a score based on how binding is influenced by mutations. From these scores, the relative contribution of each position to the overall binding is calculated. Starting with the highest relative contribution, positions whose score together account for the selected contribution threshold are assigned as anchor locations. As a result, a higher threshold leads to the inclusion of more positions to be considered anchors.	0.8

Tiers

Given the thresholds provided above, the Best Peptide is evaluated and binned into a tier as follows:

Tier	Citeria
Pass	Best Peptide passes the binding, expression, tsl, clonal, and anchor criteria
Subclonal	Best Peptide fails the clonal criteria but passes the binding, tsl, and anchor criteria
LowExpr	Best Peptide meets the Low Expression Criteria and passes the binding, tsl, clonal, and anchor criteria
NoExpr	Best Peptide is not expressed (RNA Expr == 0 or RNA VAF == 0)
Poor	Best Peptide doesn’t fit in any of the above tiers, usually if it fails two or more criteria or if it fails the binding criteria

Criteria Details

Binding Criteria	Pass if Best Peptide is a strong binder	IC50 MT < binding_threshold and %ile MT < percentile_threshold (if --percentile-threshold parameter is set)
Expression Criteria	Pass if Best Transcript is expressed	Allele Expr > trna_vaf * expn_val
Low Expression Criteria	Peptide has low expression or no expression but RNA VAF and coverage	(0 < Allele Expr < trna_vaf * expn_val) OR (RNA Expr == 0 AND RNA Depth > trna_cov AND RNA VAF > trna_vaf)
TSL Criteria	Pass if Best Transcript has good transcript support level	TSL <= maximum_transcript_support_level
Clonal Criteria	Best Peptide is likely in the founding clone of the tumor	DNA VAF > tumor_purity / 4

aggregated.tsv.reference_matches Report Columns

This file is only generated when the --run-reference-proteome-similarity option is chosen.

Column Name	Description (BLAST)	Description (reference fasta)
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
MT Epitope Seq	The mutant peptide sequence for the epitope candidate
Peptide	The peptide sequence submitted to BLAST	The peptide sequence to search for in the reference proteome
Hit ID	The BLAST alignment hit ID (reference proteome sequence ID)	The FASTA header ID of the entry where the match was made
Hit Definition	The BLAST alignment hit definition (reference proteome sequence name)	The FASTA header description of the entry where the match was made
Match Window	The substring of the Peptide that was found in the Match Sequence
Match Sequence	The BLAST match sequence	The FASTA sequence of the entry where the match was made
Match Start	The match start position of the Match Window in the Match Sequence
Match Stop	The match stop position of the Match Window in the Match Sequence