How to set up Autoconvert in the iScan Control Software

1. In the iScan Control Software (ICS), navigate to Tools > Options:
2. In the Autoconvert Tab, check the box “Enable Autoconvert.”
3. In the AutoConvert Mapping dialog box, select Browse to navigate to the Mapping File desired or to the Mapping File to edit, or select New to create a new Mapping File.

4. To create a new Mapping File, in the AutoConvert Mapping window, designate the part number and path to the Manifest and Cluster File. Make sure the part number is for the BeadChip itself, not the BeadChip Box part number. The BeadChip part number is located on the BeadChip foil pack.
5. Select OK to save.

6. If the Part Number, Manifest file, and Cluster file are set correctly, ICS is now configured to convert IDATs to GTC files for this specific BeadChip during scanning. Repeat this process as needed for any additional BeadChips that require Autoconvert.

Additional directions are found on the iScan System page on the Illumina website: navigate to Software Configuration (Configure iScan Control Software (ICS) > Generate Normalized Data and Genotype Calls.

For any feedback or questions regarding this article (Illumina Knowledge Article #1498), contact Illumina Technical Support [e-mail].