# Can Genotype Call (GTC) files be used as input for GenomeStudio?

When using GTC files instead of intensity data (IDAT) files as input for creating a GenomeStudio workspace, a sample sheet must be used.

* Create a project sample sheet if one is not already available. For reference, see [Sample sheet guidelines for GenomeStudio](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000003223).
* Proceed to GenomeStudio project creation. During project creation in GenomeStudio v2.0.5:

1. Select "Use sample sheet to load sample intensities" in Project Wizard then select **Next**.

· GTC files cannot be used as input when the "Load sample intensities by selecting directories with intensity files" option is selected.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-8a06a5e638f6c7bc3f63563f96b6477d87646369%2Fimage1.png?alt=media)

2. Browse to the .csv sample sheet.
3. Browse to the data repository folder where the .gtc files are saved.

· When the data repository/source folder contains both .idat and .gtc files, GenomeStudio will preferentially load the .gtc files.

· Ideally, save .gtc and .idat files in separate folders.

4. Browse to the manifest repository (folder where the .bpm manifest is located).

· To prevent discrepancies in the genotype calls, make sure that this .bpm manifest is the same .bpm manifest used to generate the GTC files. 5. Select Next.

6. If a cluster file is available, check the box next to "Import cluster positions from a cluster file" and browse to the .egt cluster file.

· To prevent discrepancies, make sure that this .egt cluster file is the same .egt cluster file used to generate the GTC files.

7. Select Finish.

**Note**: Genotype Call (GTC) files can be generated for genotyping arrays, but not for methylation array data. Methylation array data is analyzed using GenomeStudio v2011.1.

**Additional resources:**

· [Sample sheet guidelines for GenomeStudio](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000003223)

· [Which files are required and optional when creating a GenomeStudio project?](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000002888)

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