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	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: - Unique for the run. - 1–70 characters. - No spaces. - 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. - Cannot be called all, default, none, unknown, undetermined, stats, or reports. - 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.
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.