> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000003223.md).
# Sample sheet guidelines for GenomeStudio Genotyping and Methylation
**GenomeStudio Genotyping Sample Sheet**
A GenomeStudio Genotyping sample sheet is a comma delimited text file (\*.csv) that identifies the sample name/ID, beadchip, and array location of each sample in a project. Sample sheet templates are available to download from the various Product Support Files pages for the various beadchip types at Illumina.com. For example, the sample sheet used to create the demo Global Screening Array v3 project can be downloaded here:\
[Infinium Global Screening Array v3.0 Support Files](https://support.illumina.com/downloads/infinium-global-screening-array-v3-0-support-files.html)
Following is a screenshot of the demo GSA v3 project samplesheet, viewed in Excel:
\*\* \
Figure 1:\*\* Screenshot - GSA-24v3-0\_A1\_SampleSheet\_Demo\_12.csv
There are three sections in a sample sheet, "Header", "Manifests", and "Data".
* "Header" is not required, and is user-defined
* "Manifests" contains two columns; the first contains the letter A, the second is populated by the name of the .bpm manifest file to be applied in creating the project, excluding the .bpm extension
* "Data" contains the following columns
**Table** **1**: Genotyping Column headings - Data section
| Column | Description | Optional (O) or
Required (R)
|
| ------------------ | ------------------------------------------------------------------------------------------------------------------------ | -------------------------------------- |
| Sample\_ID | Sample identifier (used only for display in the table). | R |
| SentrixBarcode\_A | The barcode of the Array that this sample was hybridized to | R |
| SentrixPosition\_A | The position within the Array this sample was hybridized to | R |
| Sample\_Name | Name of the sample (used only for display in the table). | O |
| Sample\_Plate | The barcode of the sample plate for this sample (used only for display in thetable). | O |
| Sample\_Well | The well within the sample plate for this sample (used only for display in thetable). | O |
| Gender | Male, Female, or Unknown. | O |
| Sample\_Group | A group, if any, that this sample belongs to
(used for exclusion in the Final
ReportWizard).
| O |
| Replicates | The Sample\_ID of a sample that is a
replicate to this sample (used in
reproducibility error calculations).
| O |
| Parent1 | The Sample\_ID of the first parent for this
sample.
| O |
| Parent2 | The Sample\_ID of the second parent for
this sample.
| O |
| Path | Directory where your data are stored. | O |
| Reference | Used for paired sample analysis. Populate this column with the sample ID of the reference sample. | O |
In order to avoid errors during the project creation step, follow the guidelines below for creating a sample sheet.
* The format of the sample must match the template, including the complete header section, the data section, and all column names.
* Fill in the **required** columns: Sample ID, Sentrix\_ID, and Sentrix\_Position. Other columns are optional (See Table 1).
* The Sentrix ID and Sentrix Position must match the intensity data (.idat) files that will be loaded to create the project.
* Only list samples that have the .idat files in the parent folder. Do not list any other samples.
* File names must only contain alphanumeric characters, underscores, and dashes. Introducing invalid characters, such as spaces or symbols (i.e. “@” or “#” ) will result in errors.
* The manifest name in the sample sheet must match the exact filename of the .bpm file that will be used for the analysis.
* If using Excel, make sure barcodes are not displayed in scientific notation. Excel will automatically convert the BeadChip barcodes to scientific notation and will not save to the .csv file correctly. The BeadChip barcodes must be formatted correctly before saving (every time the file is saved). Please see the following article for more information regarding correctly formatting barcodes:\
[Important information about using 12-digit BeadChip barcodes in GenomeStudio sample sheets](/microarray/general/microarray-general-reference_material-list/000001422.md)
* Save the sample sheet as a comma separated value text file (\*.csv).
* Check the final sample sheet for accuracy by opening it with Notepad.
* Make sure that the delimiter is a comma. GenomeStudio is unable to parse a sample sheet if semi-colons, tabs, or other delimiters are present in the file.
* Check for extra lines with blank information. These lines are identified by GenomeStudio as additional samples and are not visible when viewed in Excel (but can be seen in a standard text editor like Notepad). Remove the extra lines from the sample sheet by selecting and deleting them in Notepad.
* If the sample sheet is not recognized, rename the sample sheet with a simple name, such as Sample\_Sheet.csv.
**GenomeStudio Methylation Module Sample Sheet**
There are some key differences between a Methylation Module sample sheet and a Genotyping Sample Sheet
* The Methylation Module sample sheet does not have a "Manifest" sectioni
* The column headings in the "Data" section have different names
* Certain columns are required to be present, but not to contain information
**Table 2:** Methylation column headings - Data section
| Column | Description | Optional (O) or
Required (R)
|
| ----------------- | ------------------------------------------------------------------------------------------------ | -------------------------------------- |
| Sample\_Name | Name of the sample | O |
| Sentrix\_ID | The barcode of the Array that this sample was hybridized to | R |
| Sentrix\_Position | The position within the Array this sample was hybridized to | R |
| Sample\_Plate | The barcode of the sample plate for this sample (used
only for display in the table)
| O |
| Sample\_Group | User-specified name of the sample group - The column must be present, but data entry is optional | R |
| Pool\_ID | Legacy column -Column must be present on sample sheet, but should not contain any information | R |
**Figure 2:** Screenshot - MethylationEPIC sample sheet
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| *For any feedback or questions regarding this article (Illumina Knowledge Article #3223), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001422%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |
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