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How to generate VCF from Illumina BeadArray data

To generate VCFs from Illumina BeadArray data, users have three options:
ACLI: Use the Illumina software "Array Analysis CLI" (ACLI). This software uses a command line interface to generate gtc and vcf files from raw scanner intensity data. As in the other methods, it requires a manifest and cluster file, as it does not have the clustering capability of GenomeStudio. It is a one-stop shop compared to the other methods.
Here is the support page containing links to download the software as well as links to documentation:
PLINK: Export data to PLINK and then use PLINK to generate the vcf:
  1. 1.
    Download the PLINK Input Report Plug-in v2.1.4 from the GenomeStudio Software Downloads page
  2. 2.
    Open GenomeStudio project
  3. 3.
    Go to Analysis > Reports > Report Wizard
  4. 4.
    Select Custom Report and under the dropdown select PLINK Input Report
  5. 5.
    Export PLINK report in .ped file format
  6. 6.
    Import .ped file into PLINK to generate vcf file. See this page for more info regarding the related procedure:
Beeline + Github Tool
  1. 1.
    Use Beeline to convert .idat files to .gtc files (For further information please search for Knowledge Base Article Infinium Genotyping: Introduction to Beeline 2.0 and Data Analysis Workflows Support Webinar Video webinar for more details on how to use Beeline)
  2. 2.
    Use the GitHub tool "GTCtoVCF" to convert .gtc to .vcf (
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. For additional questions regarding the tool, Customers are encouraged to post on the github issue board for the project so the developers can help with troubleshooting.
For any feedback or questions regarding this article (Illumina Knowledge Article #3079), contact Illumina Technical Support [email protected].
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