How to generate VCF from Illumina BeadArray data

To generate VCFs from Illumina BeadArray data, users have several options:

DRAGEN Array (recommended): The Illumina DRAGEN Array Local software uses a command line interface to generate GTC and VCF files from raw scanner intensity data (IDAT). Analysis requires a manifest and cluster file, as it does not have the clustering capability of GenomeStudio. See DRAGEN Array Support Resources page to download the Windows or Linux installer. Refer to the DRAGEN Array User Guide for instructions on how to carry out the Local Analysis. For additional information on compatible GTC files, see Illumina Knowledge article "What GTC files can be used with DRAGEN Array Local?"

Array Analysis CLI (ACLI): ACLI is the predecessor to DRAGEN Array with similar functionality. ACLI also uses a command line interface to generate GTC and VCF files from IDATs. It is recommended to use DRAGEN Array which has additional features compared to ACLI. See the ACLI Support Resources page to download the Windows, Linux, or Mac installer. Refer to the Product Documentation for instructions on how to carry out the analysis.

Beeline + Github Tool

1. Use Beeline to convert IDAT files to GTC files (see Knowledge Base Article Infinium Genotyping: Introduction to Beeline 2.0 and Data Analysis Workflows Support Webinar Video for more details on how to use Beeline).

2. Use the GitHub tool "GTCtoVCF" to convert .gtc to .vcf (https://github.com/Illumina/GTCtoVCF).

The GitHub tool is Linux-based. Users that do not have a Linux OS can create a virtual machine on Windows to run a Linux based operating system like Ubuntu.

Note: The GitHub GTCtoVCF converter tool is considered semi-archived. As of May 2023, it is recommended to use the fully-supported Illumina solution DRAGEN Array for IDAT to GTC to VCF conversion.

PLINK: Export data to PLINK and then use PLINK to generate the VCF:

1. Download the PLINK Input Report Plug-in v2.1.4 from the GenomeStudio Software Downloads page

2. Open GenomeStudio project

3. Go to Analysis > Reports > Report Wizard

4. Select Custom Report and under the dropdown select PLINK Input Report

5. Export PLINK report in .ped file format

6. Import .ped file into PLINK to generate VCF file. See this page for more info regarding the related procedure: https://www.biostars.org/p/104814/

For any feedback or questions regarding this article (Illumina Knowledge Article #3079), contact Illumina Technical Support [e-mail].