# Sample Sheet Requirements

The TN pipeline may contain additional user defined fields such as Sex, Tumor Type or Case ID for use with variant interpretation in ICI.

## Standard Sample Sheet Requirements

The following sample sheet requirements describe required and optional fields for TN pipeline. It must contain fhe follwing sections.

> **The analysis fails if the sample sheet requirements are not met.**

### \[Header] Section

| Parameter         | Required | Details                |
| ----------------- | -------- | ---------------------- |
| FileFormatVersion | 2        | v2 sample sheet format |

### \[TN\_Data] Section

| Sample Parameter       | Required | Details                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| ---------------------- | -------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Sample\_ID             | Required | <p>The unique ID to identify a sample. The sample ID is included in the output file names. Sample IDs are not case sensitive. Sample IDs must have the following characteristics:<br>- Unique for the run.<br>- 1–70 characters.<br>- No spaces.<br>- Alphanumeric characters with underscores and dashes. If you use an underscore or dash, enter an alphanumeric character before and after the underscore or dash. eg, Sample1-T5B1\_022515.<br>- Cannot be called <code>all</code>, <code>default</code>, <code>none</code>, <code>unknown</code>, <code>undetermined</code>, <code>stats</code>, or <code>reports</code>.<br>- Must match a Sample\_ID listed in the \[BCLConvert\_Data] section. Each sample must have a unique combination of Lane (if applicable), sample ID, and index ID or the analysis will fail.</p> |
| Case\_ID               | Required | A unique ID that links the same biological samples from the same individual. It is used for variant interpretation in downstream software such as the Illumina Connected Insights software                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
| Sample\_Type           | Required | Possible value is DNA.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
| Sample\_Classification | Required | Possible values are Tumor or Normal.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
| Specimen\_Type         | Required | Possible values are FFPE (Formalin-Fixed, Paraffin-Embedded), FF (Fresh Frozen) for Tumor sample classification. No restrictions on a sample classification of Normal                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
| Sex                    | Optional | Possible values are Male, Female or Unknown                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| Tumor\_Type            | Optional | Support tumor type code based on the SNOMED ontology                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
| Sample\_Description    | Optional | Free text description for the sample                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |

To ensure a successful analysis, follow these guidelines:

1. Avoid any blank lines at the end of the sample sheet; these can cause the analysis to fail.
2. When running local analysis using the command line save the sample sheet in the sequencing run folder with the default name `SampleSheet.csv`, or choose a different name and specify the path in the command-line options.


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