Output data

Neoantigens

NeoFox returns the neoantigen candidates and their annotated features as output. Two output formats are supported: tabular format or JSON format. The user gets the neoantigen annotations in all formats. Despite different structures, both formats provide the same content with the exception of the metadata on the annotations which is only present in the JSON format.

The following table describes each of the annotations in the output:

TABLE 1

Column name	Description	Feature group/ Paper
dnaVariantAlleleFrequency	the variant allele frequency calculated from the DNA
mutatedXmer	the long mutated amino acid sequence
wildTypeXmer	the long non-mutated amino acid sequence. This field shall be empty for alternative neoantigen classes
patientIdentifier	the patient identifier
rnaExpression	the RNA expression. If expression was imputed, this will will be imputedGeneExpression	expression
imputedGeneExpression	median gene expression in the TCGA cohort of the tumor entity provided in the patient file.	expression
rnaVariantAlleleFrequency	the variant allele frequency calculated from the RNA
gene	the HGNC gene symbol
Mutated_rnaExpression_fromRNA	transcript expression normalized by the variant allele frequency in RNA of the mutation	expression
Mutated_rnaExpression_fromDNA	transcript expression normalized by the variant allele frequency in DNA of the mutation
Mutated_imputedGeneExpression_fromRNA	imputeted gene expression normalized by the variant allele frequency in RNA of the mutation	expression
Mutated_imputedGeneExpression_fromDNA	imputed gene expression normalized by the variant allele frequency in RNA of the mutation
mutation_not_found_in_proteome	indicates if mutated amino acid sequence was not found in the WT proteome by exact search	Priority score
NetMHCpan_bestRank_rank	minimal MHC I binding rank score over all neoepitope candidates (8-11mers) and MHC I alleles	MHC I binding with netMHCpan
NetMHCpan_bestRank_peptide	neoepitope candidate sequence with minimal MHC I binding rank score	MHC I binding with netMHCpan
NetMHCpan_bestRank_core	The minimal 9 amino acid binding core directly in contact with the MHC.	MHC I binding with netMHCpan
NetMHCpan_bestRank_Icore	Interaction core. This is the sequence of the binding core including eventual insertions of deletions.	MHC I binding with netMHCpan
NetMHCpan_bestRank_Of	Starting position offset of the core in the peptide (0 based)	MHC I binding with netMHCpan
NetMHCpan_bestRank_Gp	Position of the deletion (0 based), if any, in the Icore compared to the core.	MHC I binding with netMHCpan
NetMHCpan_bestRank_Gl	Length of the deletion, if any, in the Icore compared to the core.	MHC I binding with netMHCpan
NetMHCpan_bestRank_allele	the MHC I allele related to NetMHCpan_bestRank_peptide	MHC I binding with netMHCpan
NetMHCpan_bestAffinity_affinity	minimal MHC I binding affinity over all neoepitope candidates (8-11mers) and MHC I alleles	MHC I binding with netMHCpan
NetMHCpan_bestAffinity_peptide	neoepitope candidate sequence with minimal MHC I binding affinity	MHC I binding with netMHCpan
NetMHCpan_bestAffinity_core	The minimal 9 amino acid binding core directly in contact with the MHC.	MHC I binding with netMHCpan
NetMHCpan_bestAffinity_Icore	Interaction core. This is the sequence of the binding core including eventual insertions of deletions.	MHC I binding with netMHCpan
NetMHCpan_bestAffinity_Of	Starting position offset of the core in the peptide (0 based)	MHC I binding with netMHCpan
NetMHCpan_bestAffinity_Gp	Position of the deletion (0 based), if any, in the Icore compared to the core.	MHC I binding with netMHCpan
NetMHCpan_bestAffinity_Gl	Length of the deletion, if any, in the Icore compared to the core.	MHC I binding with netMHCpan
NetMHCpan_bestAffinity_allele	the MHC I allele related to NetMHCpan_bestAffinity_peptide	MHC I binding with netMHCpan
NetMHCpan_bestRank9mer_rank	minimal MHC I binding rank score over all neoepitope candidates (9mers only) and MHC I alleles	MHC I binding with netMHCpan
NetMHCpan_bestRank9mer_peptide	neoepitope candidate sequence (9mer) with minimal MHC I binding rank score	MHC I binding with netMHCpan
NetMHCpan_bestRank9mer_allele	the MHC I allele related to NetMHCpan_bestRank9mer_peptide	MHC I binding with netMHCpan
NetMHCpan_bestAffinity9mer_affinity	minimal MHC I binding affinity over all neoepitope candidates (9mers) and MHC I alleles	MHC I binding with netMHCpan
NetMHCpan_bestAffinity9mer_allele	the MHC I allele related to NetMHCpan_bestAffinity9mer_peptide	MHC I binding with netMHCpan
NetMHCpan_bestAffinity9mer_peptide	neoepitope candidate sequence (9mer) with minimal MHC I binding affinity	MHC I binding with netMHCpan
NetMHCpan_bestAffinity_affinityWT	MHC I binding affinity of NetMHCpan_bestAffinity_peptideWT	MHC I binding with netMHCpan
NetMHCpan_bestAffinity_peptideWT	WT epitope that corresponds to NetMHCpan_bestAffinity_peptide	MHC I binding with netMHCpan
NetMHCpan_bestRank_rankWT	MHC I binding rank score of NetMHCpan_bestRank_peptideWT	MHC I binding with netMHCpan
NetMHCpan_bestRank_peptideWT	WT epitope that corresponds to NetMHCpan_bestRank_peptide	MHC I binding with netMHCpan
NetMHCpan_bestRank9mer_rankWT	MHC I binding rank score of NetMHCpan_bestRank9mer_peptideWT	MHC I binding with netMHCpan
NetMHCpan_bestRank9mer_peptideWT	WT epitope that corresponds to NetMHCpan_bestRank9mer_peptide	MHC I binding with netMHCpan
NetMHCpan_bestAffinity9mer_affinityWT	MHC I binding affinity of NetMHCpan_bestAffinity9mer_peptideWT	MHC I binding with netMHCpan
NetMHCpan_bestAffinity9mer_peptideWT	WT epitope that corresponds to NetMHCpan_bestAffinity9mer_peptide
PHBR_I	harmonic mean of minimal MHC I binding rank scores of all MHC I alleles of a patient	PHBR-I
NetMHCpan_bestAffinity9mer_positionMutation	indicates position of the mutation in NetMHCpan_bestRank9mer_peptide	MHC I binding with netMHCpan
NetMHCpan_bestAffinity9mer_anchorMutated	mutation in NetMHCpan_bestRank9mer_peptide in an anchor position (i.e. position 2 or 9)	anchor/non-anchor
NetMHCIIpan_bestRank_rank	minimal MHC II binding rank score over all neoepitope candidates (15mers) and all MHC II alleles	MHC II binding with netMHCIIpan
NetMHCIIpan_bestRank_peptide	neoepitope candidate sequence with minimal MHC II binding rank score	MHC II binding with netMHCIIpan
NetMHCIIpan_bestRank_core	Binding core register (9mer)	MHC II binding with netMHCIIpan
NetMHCIIpan_bestRank_Of	Starting position offset of the optimal binding core (starting from 0)	MHC II binding with netMHCIIpan
NetMHCIIpan_bestRank_coreRel	Reliability of the binding core, expressed as the fraction of networks in the ensemble selecting the optimal core	MHC II binding with netMHCIIpan
NetMHCIIpan_bestRank_allele	the MHC II isoform related to NetMHCIIpan_bestRank_peptide	MHC II binding with netMHCIIpan
NetMHCIIpan_bestAffinity_affinity	minimal MHC II binding affinity over all neoepitope candidates (15mers) and all MHC II alleles	MHC II binding with netMHCIIpan
NetMHCIIpan_bestAffinity_peptide	neoepitope candidate sequence with minimal MHC II binding affinity	MHC II binding with netMHCIIpan
NetMHCIIpan_bestAffinity_core	Binding core register (9mer)	MHC II binding with netMHCIIpan
NetMHCIIpan_bestAffinity_Of	Starting position offset of the optimal binding core (starting from 0)	MHC II binding with netMHCIIpan
NetMHCIIpan_bestAffinity_coreRel	Reliability of the binding core, expressed as the fraction of networks in the ensemble selecting the optimal core	MHC II binding with netMHCIIpan
NetMHCIIpan_bestAffinity_allele	the MHC II isoform related to NetMHCIIpan_bestAffinity_peptide	MHC II binding with netMHCIIpan
NetMHCIIpan_bestRank_rankWT	minimal MHC II binding rank of NetMHCIIpan_bestRank_peptideWT	MHC II binding with netMHCIIpan
NetMHCIIpan_bestRank_peptideWT	WT epitope sequence (15mer) that corresponds to NetMHCIIpan_bestRank_peptide	MHC II binding with netMHCIIpan
NetMHCIIpan_bestAffinity_affinityWT	minimal MHC II binding rank of NetMHCIIpan_bestAffinity_peptideWT	MHC II binding with netMHCIIpan
NetMHCIIpan_bestAffinity_peptideWT	WT epitope sequence (15mer) that corresponds to NetMHCIIpan_bestAffinity_peptide	MHC II binding with netMHCIIpan
PHBR_II	harmonic mean of minimal MHC II binding rank scores of all MHC II alleles of a patient	PHBR-II
Amplitude_MHCI_bestAffinity9mer	ratio of NetMHCpan_bestAffinity9mer_affinity and NetMHCpan_bestAffinity9mer_affinityWT	Recognition Potential
Amplitude_MHCI_bestAffinity	ratio of NetMHCpan_bestAffinity_affinityWT and NetMHCpan_bestAffinity_affinity	Generator rate
Amplitude_MHCII_bestRank	ratio of NetMHCIIpan_bestRank_rank and NetMHCIIpan_bestRank_rankWT	Generator rate
Pathogensimiliarity_MHCI_bestAffinity9mer	score representing the similarity of NetMHCpan_bestAffinity9mer_peptide to pathogen sequences in IEDB database	Recognition Potential
Pathogensimiliarity_MHCII_bestAffinity	score representing the similarity of NetMHCIIpan_bestRank_peptide to pathogen sequences in IEDB database	Recognition Potential
RecognitionPotential_MHCI_bestAffinity9mer	product of Amplitude_MHCI_affinity_9mer and Pathogensimiliarity_MHCI_affinity_9mer	Recognition Potential
DAI_MHCI_bestAffinity	difference of NetMHCpan_bestAffinity_affinityWT and NetMHCpan_bestAffinity_affinity	DAI
Classically_defined_neopeptide_MHCI	NetMHCpan_bestAffinity_peptide< 50 nM	Generator rate
Alternatively_defined_neopeptide_MHCI	NetMHCpan_bestAffinity_peptide < 5000 nM and Amplitude_MHCI_bestAffinity > 10	Generator rate
Classically_defined_neopeptide_MHCII	NetMHCIIpan_bestRank_rank < 1	Generator rate
Alternatively_defined_neopeptide_MHCII	Best_rank_MHCII_score < 4 and Amplitude_MHCII_bestRank < 2	Generator rate
GeneratorRate_CDN_MHCI	number of neoepitope candidates with MHC I binding affinity < 50 nM per neoantigen canidate	Generator rate
GeneratorRate_ADN_MHCI	number of neoepitope candidates with MHC I binding affinity < 5000 nM per neoantigen canidate 10x better affinity in comparison to corresponding WT peptide	Generator rate
GeneratorRate_MHCI	sum of GeneratorRate_CDN_MHCI and GeneratorRate_ADN_MHCI	Generator rate
GeneratorRate_CDN_MHCII	number of neoepitope candidates with MHC II binding rank score < 1 per neoantigen canidate	Generator rate
GeneratorRate_ADN_MHCII	number of neoepitope candidates with MHC II binding rank score < 4 per neoantigen candidate 4x better rank in comparison to corresponding WT peptide	Generator rate
GeneratorRate_MHCII	sum of GeneratorRate_CDN_MHCII and GeneratorRate_ADN_MHCII	Generator rate
Tcell_predictor	output score of T cell predictor model	Tcell predictor
ImprovedBinder_MHCI	ratio of NetMHCpan_MHCI_rank_bestRankWT and NetMHCpan_MHCI_rank_bestRank > 1.2	self-similarity
Selfsimilarity_MHCI_conserved_binder	score representing the similarity between NetMHCpan_bestRank_peptide and NetMHCpan_bestRank_peptideWT For conservered binder only	self-similarity
Selfsimilarity_MHCI	score representing the similarity between NetMHCpan_bestRank_peptide and NetMHCpan_bestRank_peptide	self-similarity
Selfsimilarity_MHCII	score representing the similarity between NetMHCIIpan_bestAffinity_peptide and NetMHCIIpan_bestAffinity_peptide	self-similarity
Number_of_mismatches_MCHI	number of amino acids that do no match between NetMHCpan_bestRank_peptide and NetMHCpan_bestRank_peptideWT	Priority score
Priority_score_fromDNA	combinatorial score of several features such as MHC binding, transcription expression and VAF in DNA	Priority score
Priority_score_fromRNA	combinatorial score of several features such as MHC binding, transcription expression and VAF in RNA	Priority score
Priority_score_imputed_fromDNA	combinatorial score of several features such as MHC binding, imputed gene expression and VAF in DNA	Priority score
Priority_score_imputed_fromRNA	combinatorial score of several features such as MHC binding, imputed gene expression and VAF in RNA	Priority score
IEDB_Immunogenicity_MHCI	IEDB Immunogenicity score for NetMHCpan_bestAffinity_peptide	IEDB Immunogenicity
IEDB_Immunogenicity_MHCII	IEDB Immunogenicity score for NetMHCIIpan_bestAffinity_peptide	IEDB Immunogenicity
MixMHCpred_bestScore_peptide	MHC class I neoepitope candidate sequence with maximum MixMHCpred score over all neoepitope canidates (8-11mers) and MHC I alleles	MixMHCpred
MixMHCpred_bestScore_score	maximum MixMHCpred score over all neoepitope canidates (8-11mers) and MHC I alleles	MixMHCpred
MixMHCpred_bestScore_rank	rank that corresponds to MixMHCpred_bestScore_score	MixMHCpred
MixMHCpred_bestScore_allele	the allele with maximum MixMHCpred score	MixMHCpred
MixMHC2pred_bestRank_peptide	MHC class II neoepitope candidate sequence with minimal MixMHC2pred score over all neoepitope canidates (13-18mers) and MHC II alleles	MixMHC2pred
MixMHC2pred_bestRank_rank	minimal MixMHC2pred score over all neoepitope canidates (13-18mers) and MHC II alleles	MixMHC2pred
MixMHC2pred_bestRank_allele	the MHC II isoform with minimum MixMHC2pred rank score	MixMHC2pred
Dissimilarity_MHCI	score reflecting the dissimilarity of NetMHCpan_bestAffinity_peptide to the self-proteome	dissimilarity
Dissimilarity_MHCII	score reflecting the dissimilarity of NetMHCIIpan_bestAffinity_peptide to the self-proteome	dissimilarity
Vaxrank_bindingScore	total binding score of vaxrank	vaxrank
Vaxrank_totalScore	product of total binding score and transcription expression score. Originally, the root of the number of reads supporting the mutation are used in the original implementation. To simplify, the transcript expression normalised to VAF is used.	vaxrank
Vaxrank_totalScore_imputed	product of total binding score and imputed gene expression score. Originally, the root of the number of reads supporting the mutation are used in the original implementation. To simplify, the imputed gene expression normalised to VAF is used.	vaxrank
PRIME_bestScore_allele	best predicted MHC allele by PRIME model	PRIME
PRIME_bestScore_peptide	best predicted neoepitope candidate by PRIME model	PRIME
PRIME_bestScore_rank	output rank score of PRIME model	PRIME
PRIME_bestScore_score	output score of PRIME model	PRIME
HexAlignmentScore_MHCI	the alignment score by HEX for NetMHCpan_bestAffinity_peptide	HEX
HexAlignmentScore_MHCII	the alignment score by HEX for NetMHCIIpan_bestAffinity_peptide	HEX

In addition, all logging output is appended to a log file with the suffix “:raw-html-m2r:`<folder>`/:raw-html-m2r:`<prefix>`.log“, where the folder is set by --output-folder and the prefix can be set with --output-prefix.

Tabular format

An output table with the suffix “_neoantigen_candidates_annotated.tsv“ is created.
This table contains the neoantigen candidates information, the neoantigen annotations and if some user-specific additional columns
were provided in the input table, these external annotations.

This is a dummy example:

dnaVariantAlleleFrequency	gene	imputedGeneExpression	mutatedXmer	position	wildTypeXmer	patientIdentifier	rnaExpression	rnaVariantAlleleFrequency	+-13AA(SNV)/-15_AA_toSTOP(INDEL)	ADN_MHCI	ADN_MHCII	Amplitude_MHCII_rank	Amplitude_MHCI_affinity	Amplitude_MHCI_affinity_9mer	Best_affinity_MHCII_allele	Best_affinity_MHCII_allele_WT	Best_affinity_MHCII_epitope	Best_affinity_MHCII_epitope_WT	Best_affinity_MHCII_score	Best_affinity_MHCII_score_WT	Best_affinity_MHCI_9mer_allele	Best_affinity_MHCI_9mer_allele_WT	Best_affinity_MHCI_9mer_anchor_mutated	Best_affinity_MHCI_9mer_epitope	Best_affinity_MHCI_9mer_epitope_WT	Best_affinity_MHCI_9mer_position_mutation	Best_affinity_MHCI_9mer_score	Best_affinity_MHCI_9mer_score_WT	Best_affinity_MHCI_allele	Best_affinity_MHCI_allele_WT	Best_affinity_MHCI_epitope	Best_affinity_MHCI_epitope_WT	Best_affinity_MHCI_score	Best_affinity_MHCI_score_WT	Best_rank_MHCII_score	Best_rank_MHCII_score_WT	Best_rank_MHCII_score_allele	Best_rank_MHCII_score_allele_WT	Best_rank_MHCII_score_epitope	Best_rank_MHCII_score_epitope_WT	Best_rank_MHCI_9mer_allele	Best_rank_MHCI_9mer_allele_WT	Best_rank_MHCI_9mer_epitope	Best_rank_MHCI_9mer_epitope_WT	Best_rank_MHCI_9mer_score	Best_rank_MHCI_9mer_score_WT	Best_rank_MHCI_score	Best_rank_MHCI_score_WT	Best_rank_MHCI_score_allele	Best_rank_MHCI_score_allele_WT	Best_rank_MHCI_score_epitope	Best_rank_MHCI_score_epitope_WT	CDN_MHCI	CDN_MHCII	DAI_MHCI_affinity_cutoff500nM	Dissimilarity_MHCI_cutoff500nM	Expression_mutated_transcript	Generator_rate	IEDB_Immunogenicity_MHCI_cutoff500nM	Improved_Binder_MHCI	MixMHC2pred_best_allele	MixMHC2pred_best_peptide	MixMHC2pred_best_rank	MixMHCpred_best_allele	MixMHCpred_best_peptide	MixMHCpred_best_rank	MixMHCpred_best_score	Number_of_mismatches_MCHI	PHBR-I	PHBR-II	Pathogensimiliarity_MHCI_affinity_9mer	Priority_score	Recognition_Potential_MHCI_affinity_9mer	Selfsimilarity_MHCI_conserved_binder	Tcell_predictor_score_cutoff500nM	VAF_in_RNA	VAF_in_tumor	[WT]_+-13AA(SNV)/-15_AA_toSTOP(INDEL)	mutation_not_found_in_proteome	patient	substitution	transcript_expression	vaxrank_binding_score	vaxrank_total_score
0.294	BRCA2	0.5	AAAAAAAAAAAAAFAAAAAAAAAAAAA	14	AAAAAAAAAAAAALAAAAAAAAAAAAA	Ptx	0.51950689	0.857	AAAAAAAAAAAAAFAAAAAAAAAAAAA	0	1	28	0.88723	0.88723	HLA-DQA10401-DQB10402	HLA-DQA10401-DQB10402	AAAAFAAAAAAAAAA	AAAALAAAAAAAAAA	251.77	513.02	HLA-C*16:01	HLA-C*16:01	1	AAAAAAAAF	AAAAAAAAL	9	24.3	21.7	HLA-C*16:01	HLA-C*16:01	AAAAAAAAF	AAAAAAAAL	24.3	21.7	0.05	1.4	HLA-DQA10301-DQB10402	HLA-DQA10301-DQB10402	AAAAFAAAAAAAAAA	AAAALAAAAAAAAAA	HLA-C*16:01	HLA-C*16:01	AAAAAAAAF	AAAAAAAAL	0.0592	0.0493	0.0592	0.0493	HLA-C*16:01	HLA-C*16:01	AAAAAAAAF	AAAAAAAAL	1	1	-2.6	1	0.44522	1	0.18288	0	DPA1_01_03__DPB1_04_01	AAAAFAAAAAAAAAAA	0.997	B0702	AAAAAAAAF	0.1	0.50487	1	0.31193	0.21892	0	0.07017	0	0.99178271	0.40327581	0.857	0.294	AAAAAAAAAAAAALAAAAAAAAAAAAA	1	Ptx	I547T	0.51950689	3.7689	1.678
0.173	BRCA2	0.5	AAAAAAAAAAAAAMAAAAAAAAAAAAA	14	AAAAAAAAAAAAARAAAAAAAAAAAAA	Ptx	0.71575659	0.556	AAAAAAAAAAAAAMAAAAAAAAAAAAA	1	1	10	90.685	90.685	HLA-DQA10401-DQB10402	HLA-DQA10401-DQB10402	AAAAAAAAAMAAAAA	AAAAAAAAARAAAAA	421.53	554.92	HLA-C*16:01	HLA-C*16:01	1	AAAAAAAAM	AAAAAAAAR	9	24.1	6346.9	HLA-C*16:01	HLA-C*16:01	AAAAAAAAM	AAAAAAAAR	24.1	6346.9	0.25	2.5	HLA-DQA10401-DQB10302	HLA-DQA10401-DQB10302	AAAAAAAAAAMAAAA	AAAAAAAAAARAAAA	HLA-C*16:01	HLA-C*16:01	AAAAAAAAM	AAAAAAAAR	0.0587	8.9317	0.0587	8.9317	HLA-C*16:01	HLA-C*16:01	AAAAAAAAM	AAAAAAAAR	1	1	6322.8	1	0.39796	1	0.18288	1	DPA1_01_03__DPB1_04_01	AAAAMAAAAAAAAAAA	2.44	B0702	AAAAAAAAM	0.07	0.5444	1	0.29303	1.5594	0	0.10626	0	NA	0.46452844	0.556	0.173	AAAAAAAAAAAAARAAAAAAAAAAAAA	1	Ptx	E135S	0.71575659	3.8741	1.5417

JSON format

An output file with the suffix “_neoantigen_candidates_annotated.json“ is created.
This file contains neoantigen candidates information in JSON format.
The names within the models are described in TABLE 1.

This is a dummy example of a “_neoantigen_candidates.json“ file.
This file contains a list of neoantigen candidate models (for further information, please see here.
To simplify, only one full neoantigen candidate model is shown:

[{
    "patient_identifier": "Ptx",
    "gene": "BRCA2",
    "position": [14],
    "wild_type_xmer": "AAAAAAAAAAAAALAAAAAAAAAAAAA",
    "mutated_xmer": "AAAAAAAAAAAAAFAAAAAAAAAAAAA",
    "rna_expression": 0.5195068939999999,
    "imputed_gene_expression": 0.5,
    "dna_variant_allele_frequency": 0.294,
    "rna_variant_allele_frequency": 0.857,
    "neofox_annotations": [...],
    "external_annotations": [...]
}, {
    "patient_identifier": "Ptx",
    "gene": "BRCA2",
    "position": [14],
    "wild_type_xmer": "AAAAAAAAAAAAARAAAAAAAAAAAAA",
    "mutated_xmer": "AAAAAAAAAAAAAMAAAAAAAAAAAAA",
    "rna_expression": 0.715756594,
    "imputed_gene_expression": 0.5,
    "dna_variant_allele_frequency": 0.17300000000000001,
    "rna_variant_allele_frequency": 0.556,
    "neofox_annotations": [ ... ],
    "external_annotations": [ ... ]
}]

Notice that for simplicity purposes both fields neofox_annotations and external_annotations are not shown above. For further information, please see here.

This is a dummy example of the field neofox_annotations.

{
    "annotations": [{
        "name": "NetMHCpan_MHCI_rank_bestRank",
        "value": "0.0592"
    }, {
        "name": "NetMHCpan_MHCI_rank_peptide",
        "value": "AAAAAAAAF"
    }],
    "annotator": "Neofox",
    "annotator_version": "1.0.0",
    "timestamp": "20201211115212061465"
}

And this is a dummy example of the field external_annotations:

[
  {
        "name": "external_annotation_1",
        "value": "0.857"
    }, {
        "name": "external_annotation_2",
        "value": "that"
    }
]

The metadata on the annotations will look as follows:

{
 annotator: "NeoFox",
 annotator_version: "0.5.4",
 timestamp: "20211104154037935536",
 resources: [
  {
   name: "netMHCpan",
   version: "4.1"
  },
  {
   name: "netMHCIIpan",
   version: "4.0"
  },
  {
   name: "mixMHCpred",
   version: "2.1"
  },
  {
   name: "mixMHC2pred",
   version: "1.2"
  },
  {
   name: "IEDB",
   url: "http://www.iedb.org/downloader.php?file_name=doc/tcell_full_v3.zip",
   hash: "d225ab671ef375400d387354a5f450ff",
   download_timestamp: "20211103221051"
  },
  {
   name: "Human Ensembl proteome",
   version: "2021_03",
   url: "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640/UP000005640_9606.fasta.gz",
   hash: "a41303fd38380ca0321cf8a3d9beb4bc",
   download_timestamp: "20211103221051"
  },
  {
   name: "Mouse Ensembl proteome",
   version: "2021_03",
   url: "https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000000589/UP000000589_10090.fasta.gz",
   hash: "27a5de8c1eca42eebaf56400945cf7cb",
   download_timestamp: "20211103221051"
  },
  {
   name: "IMGT/HLA database",
   version: "3.46.0",
   url: "https://raw.githubusercontent.com/ANHIG/IMGTHLA/Latest/Allelelist.txt",
   hash: "5a7618819498b88d0790bf4d58975d13",
   download_timestamp: "20211103221051"
  }
 ]
}

Neoepitopes

NeoFox returns the neoepitopes candidates and their annotated features as output when using
the flag --with-all-neoepitopes or when explicitly annotating neoepitopes with the command neofox-epitope. Two output formats are supported: tabular format or JSON format. The user gets the neoepitope annotations in all formats. Despite different structures, both formats provide the same content with the exception of the metadata on the annotations which is only present in the JSON format. The tabular format is split into two tables:
a first one for the MHC-I neoepitope candidates and a second one for
the MHC-II neoepitope candidates.

Tabular format

Two output files with the suffix “_mhcI_epitope_candidates_annotated.tsv” and “”_mhcII_epitope_candidates_annotated.tsv”” are created.

The following table describes each of the annotations in the output. MHC-I or MHC-II specific features will be only available in the respective table:

TABLE 2

JSON format

Only when using the command neofox-epitope an output file with the suffix “_neoepitope_candidates_annotated.json“ is created.
This file contains neoepitope candidates information in JSON format.
The names within the models are described in TABLE 2.

This is a dummy example of a “_neoantigen_candidates.json“ file.
This file contains a list of neoantigen candidate models (for further information, please see here.
To simplify, only one full neoantigen candidate model is shown:

[{
    "patient_identifier": "Ptx",
    "gene": "BRCA2",
    "mutated_peptide": "AAAALAAAA",
    "wild_type_peptide": "AAAAFAAAA",
    "allele_mhc_i": "HLA-A*01:01",
    "rna_expression": 0.519,
    "imputed_gene_expression": 0.5,
    "dna_variant_allele_frequency": 0.294,
    "rna_variant_allele_frequency": 0.857,
    "affinity_mutated": 2.567,
    "rank_mutated": 0.898,
    "affinity_wild_type": 1.023,
    "rank_wild_type": 2.398,
    "neofox_annotations": [...],
    "external_annotations": [...]
}, {
    "patient_identifier": "Ptx",
    "gene": "BRCA2",
    "mutated_peptide": "AAAAAAAAAAAAARAAAAAAAAAAAAA",
    "wild_type_peptide": "AAAAAAAAAAAAAMAAAAAAAAAAAAA",
    "isoform_mhc_i_i": "DRB1*01:01",
    "rna_expression": 0.715,
    "imputed_gene_expression": 0.5,
    "dna_variant_allele_frequency": 0.173,
    "rna_variant_allele_frequency": 0.556,
    "affinity_mutated": 2.567,
    "rank_mutated": 0.898,
    "affinity_wild_type": 1.023,
    "rank_wild_type": 2.398,
    "neofox_annotations": [ ... ],
    "external_annotations": [ ... ]
}]

Notice that for simplicity purposes both fields neofox_annotations and external_annotations are not shown above. For further information, please see here.
For an example of the NeoFox annotations section, see the previous section.