---
title: Oncology Analytics inputs and parameters
description: >-
  VCF formats, HLA types, peptide sequences, and configuration options for the
  oncology analytics tools.
tags:
  - oncology
  - inputs
---

> **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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