Oncology Analytics inputs and parameters
VCF formats, HLA types, peptide sequences, and configuration options for the oncology analytics tools.
oncologyinputs
Retired tools
hrd_score, liquid_biopsy_ctdna and tumor_fraction_estimate are retired and can no longer be run, so their outputs are no longer produced. Use an allele-specific copy-number HRD caller such as scarHRD for HRD, ichorCNA on low-pass WGS for tumor fraction, and a dedicated ctDNA/MRD pipeline for ctDNA.
You provide VCF variant calls, mutation lists, peptide sequences, or HLA alleles depending on the tool; matching the right input type and genome build to your sample most shapes whether the clinical thresholds apply cleanly.
Common input formats
Most oncology tools accept one of these input types:
| Input Type | Format | Example | Accepted By |
|---|---|---|---|
| VCF file | Standard VCF 4.x | Somatic variant calls | tmb_msi_calculate, neoantigen_predict |
| Mutation list | Chrom, pos, ref, alt | chr7, 55259515, T, G | tmb_msi_calculate, neoantigen_predict |
| Peptide sequences | Amino acid strings | YLQPRTFLL (8-25mer) | mhc_binding_predict |
| HLA alleles | Standard nomenclature | HLA-A*02:01 | mhc_binding_predict, neoantigen_predict |
TMB/MSI Calculate parameters
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
mutations | array or file | Yes | -- | Somatic mutations (VCF or structured list) |
genome_build | string | No | "GRCh38" | Reference genome build |
panel_size_mb | number | No | null | Sequencing panel size in megabases (null = WES/WGS) |
coding_only | boolean | No | true | Count only coding region mutations for TMB |
min_vaf | number | No | 0.05 | Minimum variant allele frequency (0-1) |
min_depth | integer | No | 20 | Minimum read depth at variant site |
msi_sites | array | No | Auto-selected | Custom microsatellite loci to evaluate |
TMB calculation modes
| Mode | Panel Size | Description |
|---|---|---|
| WGS | null or 3000+ Mb | Whole genome, most accurate |
| WES | null or 30-60 Mb | Whole exome, standard clinical |
| Targeted panel | 0.5-10 Mb | Panel-specific normalization applied |
MSI classification thresholds
| Status | Unstable Sites | Description |
|---|---|---|
| MSS | < 10% | Microsatellite stable |
| MSI-L | 10-30% | Low microsatellite instability |
| MSI-H | ≥ 30% | High microsatellite instability |
MHC Binding Predict parameters
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
peptides | string[] | Yes | -- | Peptide sequences (8-25 amino acids each) |
hla_alleles | string[] | Yes | -- | HLA alleles in standard nomenclature |
mhc_class | string | No | "I" | MHC class: "I" (8-11mer) or "II" (13-25mer) |
method | string | No | "netmhcpan" | Prediction method: "netmhcpan", "mhcflurry" |
binding_threshold | number | No | 500 | Weak binding threshold in nM |
Common HLA alleles
| Allele | Frequency (Caucasian) | Peptide Length |
|---|---|---|
HLA-A*02:01 | 27.5% | 9-10mer |
HLA-A*01:01 | 16.0% | 9-10mer |
HLA-A*03:01 | 13.5% | 9-10mer |
HLA-B*07:02 | 12.0% | 9-10mer |
HLA-B*08:01 | 10.5% | 8-10mer |
HLA-C*07:01 | 15.5% | 9mer |
Peptide length guidelines
| MHC Class | Optimal Length | Accepted Range |
|---|---|---|
| Class I | 9mer | 8-11mer |
| Class II | 15mer | 13-25mer |
Neoantigen Predict parameters
| Parameter | Type | Required | Default | Description |
|---|---|---|---|---|
mutations | array or file | Yes | -- | Somatic mutations (VCF or structured list) |
hla_alleles | string[] | Yes | -- | Patient HLA alleles (up to 6 class I) |
expression_data | file | No | -- | RNA-seq expression values (TPM) |
genome_build | string | No | "GRCh38" | Reference genome build |
peptide_lengths | integer[] | No | [8, 9, 10, 11] | Peptide lengths to generate |
binding_threshold | number | No | 500 | Maximum IC50 for candidate selection (nM) |
min_expression | number | No | 1.0 | Minimum gene expression (TPM) for filtering |
include_clonality | boolean | No | true | Include clonality assessment in ranking |
Neoantigen ranking criteria
| Criterion | Weight | Description |
|---|---|---|
| MHC binding affinity | High | IC50 < 50 nM strongly preferred |
| Gene expression | Medium | Higher expression increases presentation likelihood |
| Clonality | Medium | Clonal mutations preferred over subclonal |
| Mutation type | Low | Missense preferred; frameshifts generate more neoantigens |
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