# TMB, MSI, GIS Input Requirement

## Tumor Mutational Burden (TMB)

| File Type | Sample File Name   | Examples                                                                                                                                                                                                                                                                                                                                       |
| --------- | ------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| JSON      | \*.tmb.json        | [Minimal](https://github.com/illumina-swi/ici-docs/blob/main/docs/configure/configuration/du-introduction/du-custom-pipeline-configuration/biomarkers/tmb-json-min.md) \| [Full](https://github.com/illumina-swi/ici-docs/blob/main/docs/configure/configuration/du-introduction/du-custom-pipeline-configuration/biomarkers/tmb-json-full.md) |
| CSV       | \*.tmb.metrics.csv | [Minimal](https://github.com/illumina-swi/ici-docs/blob/main/docs/configure/configuration/du-introduction/du-custom-pipeline-configuration/biomarkers/tmb-csv-min.md) \| [Full](https://github.com/illumina-swi/ici-docs/blob/main/docs/configure/configuration/du-introduction/du-custom-pipeline-configuration/biomarkers/tmb-csv-full.md)   |

## Microsatellite Instability (MSI)

| File Type | Sample File Name | Examples                                                                                                                                                                                                                                                                                                                                       |
| --------- | ---------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| JSON      | \*.msi.json      | [Minimal](https://github.com/illumina-swi/ici-docs/blob/main/docs/configure/configuration/du-introduction/du-custom-pipeline-configuration/biomarkers/msi-json-min.md) \| [Full](https://github.com/illumina-swi/ici-docs/blob/main/docs/configure/configuration/du-introduction/du-custom-pipeline-configuration/biomarkers/msi-json-full.md) |

## Genomic Instability Score (GIS)

| File Type | Sample File Name | Examples                                                                                                                                                                                                                                                                                                                                       |
| --------- | ---------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| JSON      | \*.gis.json      | [Minimal](https://github.com/illumina-swi/ici-docs/blob/main/docs/configure/configuration/du-introduction/du-custom-pipeline-configuration/biomarkers/gis-json-min.md) \| [Full](https://github.com/illumina-swi/ici-docs/blob/main/docs/configure/configuration/du-introduction/du-custom-pipeline-configuration/biomarkers/gis-json-full.md) |

## Homologous Recombination Deficiency Score (HRD)

| File Type | Sample File Name | Examples                                                                                                                                                            |
| --------- | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| CSV       | \*.hrdscore.csv  | [Full](https://github.com/illumina-swi/ici-docs/blob/main/docs/configure/configuration/du-introduction/du-custom-pipeline-configuration/biomarkers/hrd-csv-full.md) |

## Human Leukocyte Antigen Genotype (HLA)

| File Type | Sample File Name | Examples                                                                                                                                                            |
| --------- | ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| TSV       | \*.hla.tsv       | [Full](https://github.com/illumina-swi/ici-docs/blob/main/docs/configure/configuration/du-introduction/du-custom-pipeline-configuration/biomarkers/hla-tsv-full.md) |