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

Genotype Call (GTC) files can be used as input for GenomeStudio when creating a project. When using GTC files instead of intensity data (IDAT) files, a properly formatted sample sheet is required to define sample information and enable successful project setup.

Using GTC files allows users to work with previously generated genotype calls without reprocessing raw intensity data. However, because GTC files do not contain all the metadata needed to automatically populate a project, the sample sheet must be provided to ensure that sample identifiers and associated information are correctly assigned within GenomeStudio.

• Create a project sample sheet if one is not already available. For guidance, see Sample sheet guidelines for GenomeStudio Genotyping and Methylation.

• After preparing and validating the sample sheet, proceed with Genotyping project creation in GenomeStudio v2.0.5.

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

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

Figure 1. In Project Wizard, users must select the sample sheet option when using GTCs

1. Browse to the .csv sample sheet.

2. Browse to the data repository folder where the .gtc files are saved.

Note: When the data repository/source folder contains both .idat and .gtc files, GenomeStudio will preferentially load the .gtc files. However, it is recommended to save .gtc and .idat files in separate folders.

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

Note: To prevent discrepancies in the genotype calls, make sure that this .bpm manifest is the same .bpm manifest used to generate the GTC files.

1. Select Next.

2. 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.

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

1. 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 References:

• Which files are required and optional when creating a GenomeStudio project?

• How to identify which Manifest and Cluster Files were used to generate a GTC File

For any feedback or questions regarding this article (Illumina Knowledge Article #5917), contact Illumina Technical Support [e-mail].