Use Beeline to regenerate GTC Files with a different cluster file or manifest file

In Beeline software, users can use the original idat files and regenerate gtc files with the new cluster file and/or .bpm manifest file.

1. Download the Beeline software v.2.0.3 from the Beeline Support page.

2. Upon launching the Beeline software, a welcome screen appears with links to training resources. Select “Close” in the bottom right corner:

1. In the next screen select "Convert IDAT Files to GTC Files."

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1. Follow the instructions seen on page 11 of the Beeline Software User Guide and browse to the IDAT Folder, Manifest file, and Cluster File.

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• Note:

  • Beeline is expecting the .idat files to be contained in a folder that has the same name as the barcode of the idats, eg, 203561980081. In Beeline, you can designate the .idat folder either as the direct barcode folder, or the folder containing the barcode folder, one level up.

  • For Beeline to work, the idats need to have their original name. If the idats have been renamed, edit them back to their original name eg, "203561980081_R02C01_Red.idat."

  • If renaming the cluster file, be aware that the custom cluster file name must match the Illumina convention up to the first “underscore” -> CytoSNP-850Kv1-2_custom-text-here.egt

  • If working in GenomeStudio, you can create a new project using the new GTC files and a sample sheet (required). Regenerate the CN Metrics report and check the LogRDev values in GenomeStudio as usual.

For any feedback or questions regarding this article (Illumina Knowledge Article #2205), contact Illumina Technical Support [email protected].