How to set up Autoconvert in the iScan Control Software

Autoconvert is a standalone software application that analyzes raw intensity data (.idat files) generated from Illumina BeadChips. The software combines IDAT data with information from the corresponding BeadChip manifest (.bpm) and, optionally, a cluster file (.egt) to produce normalized intensity data. When a cluster file is included, Autoconvert also generates B Allele Frequency (BAF), Log R Ratio (LRR), and genotype calls for each assayed SNP on a per-sample basis. .gtc files (genotype call files) are per-sample output files generated by Autoconvert. These files contain normalized intensity values, B Allele Frequency (BAF), Log R Ratio (LRR), and genotype calls—the same per-sample metrics typically calculated in GenomeStudio. GTC files are stored in a compressed binary format and can be parsed by third-party tools or converted to VCF format using third-party GTC-to-VCF converters. Autoconvert can be launched directly from the iScan Control Software (ICS), enabling automatic analysis immediately after a BeadChip is scanned and IDAT files are generated. When enabled, Autoconvert analyzes the intensity data and automatically outputs GTC files. To use this feature, Autoconvert must be turned on in ICS, and a mapping file must be selected to associate each BeadChip type with the appropriate manifest and, if applicable, cluster file. 1. In the iScan Control Software, navigate to Tools > Options.

Figure 1. iScan Control Software (ICS) menu.

1. In the Autoconvert Tab, check the box “Enable Autoconvert.”

Figure 2. Enable AutoConvert checkbox.

1. In the AutoConvert Mapping dialog box, select Browse to navigate to the desired Mapping File in order to apply or edit its settings, or select New to create a new Mapping File. Mapping files are stored in the iScan Control Software directory and have the file extension ".acc"

2. To add a new BeadChip type to the active mapping file and associate it with the appropriate manifest and cluster files, click the Edit Mapping File in the AutoConvert Mapping window.

3. Next, select the "New" button at the bottom of the window. A previously blank line will be filled with "Default" values for Product Part Number, Manifest File, and Cluster File.

Figure 3. Line populated with "Default" values for Product Part Number, Manifest file, and Cluster file.

1. Determine the correct Part Number to enter for the BeadChip type. Make sure the part number is for the BeadChip itself and not the BeadChip Box part number. This is contained in the BeadChip foil pack.

Figure 4. BeadChip Part Number is not located on the BeadChip box.

Figure 5. Location of BeadChip Part Number on the BeadChip foil pack.

Note: The correct number on the foil pack is referred to as the Reference number, and is preceded by a boxed "REF".

1. In the panel on the right, under General, select PartNumber and enter the BeadChip part number. Next click the Browse button next to Manifest File Path and navigate to the manifest file to be associated with this BeadChip type. Repeat the same steps to specify the Cluster File Path.

Figure 6. Manifest File Path assigned to a BeadChip type.

1. There is an option to select an existing product listed in the mapping file to edit its settings.To update the associated manifest or cluster file, click the product Part Number in the list, then use the Browse button in the right-hand panel to select an alternate manifest or cluster file.

Figure 7. Selection ofpre-existing products.

1. Select OK to save. 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.

2. Repeat this process as needed for any additional BeadChips that require Autoconvert. Do not create a separate .acc file for each BeadChip type. Instead, create an .acc file that includes the default BeadChips and associated manifest and cluster file settings used regularly. Create alternate .acc files only when there is a recurring need to switch to different settings.

For additional instructions, refer to the iScan System page on the Illumina website and 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].