> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000003079.md).

# How to generate VCF files from Illumina BeadArray data

To generate Variant Call Format (VCF) files from Illumina BeadArray data, users have several available options depending on their analysis requirements. This article provides an overview of the supported options and outlines key considerations to help users select the most appropriate approach for their data and downstream applications.

**DRAGEN Array Local (Recommended)**

The Illumina DRAGEN Array Local software uses a command-line interface (CLI) to generate GTC and VCF files from raw scanner intensity data (IDAT) files. Analysis requires a manifest and cluster file, as it does not have the clustering capability of GenomeStudio 2.0. The Windows or Linux installer can be downloaded from [DRAGEN Array Secondary Analysis Support](https://support.illumina.com/array/array_software/dragen-array-secondary-analysis.html). Instructions for performing local analysis are available in the [DRAGEN Array Local Analysis](https://help.dragenarray.illumina.com/product-guides/dragen-array-local-analysis) documentation. For additional details on compatible GTC files, refer to the Illumina Knowledge article [What GTC files can be used with DRAGEN Array Local?](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/What-GTC-files-can-be-used-with-DRAGEN-Array-Local/README.md)

**Array Analysis Command Line Interface (ACLI)**

Array Analysis CLI (ACLI) is the predecessor to DRAGEN Array and provides command-line tools for generating GTC and VCF files from IDAT data. While ACLI offers similar core functionality, Illumina recommends DRAGEN Array Local, which includes additional features and is the currently supported solution. ACLI installers and documentation on how to carry out the analysis are available from [Illumina Microarray Analytics - Array Analysis CLI Software Downloads](https://support.illumina.com/ko-kr/array/array_software/ima-array-analysis-cli/downloads.html) and [Illumina Microarray Analytics - Array Analysis CLI Support Resources](https://support-docs.illumina.com/ARR/ArrayAnalysisCLI/Content/ARR/FrontPages/ArrayAnalysisCLI.htm).

**Note:** ACLI was obsolesced in December 2024, and support ended in July 2025. [DRAGEN Array Local](https://help.dragenarray.illumina.com/product-guides/dragen-array-local-analysis) is the supported Illumina solution for local array analysis.

**Beeline + Github Tool**

This workflow uses two separate tools to generate VCF files from Illumina BeadArray data.1. Beeline 2.0 is used to convert IDAT files to GTC files (see the Recorded Webinar available on [Infinium Genotyping - Introduction to Beeline 2.0 and Data Analysis Workflows Support Webinar Video](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Infinium-Genotyping-Introduction-to-Beeline-2-0-and-Data-Analysis-Workflows-Support-Webinar-Video/README.md) for more details on how to use Beeline).\
2\. The GitHub tool "[Illumina/GTCtoVCF](https://github.com/Illumina/GTCtoVCF)" is used to convert GTC to VCF format.

**Note:**

The GitHub Illumina/GTCtoVCF tool is Linux-based. Users without a Linux system may run the tool using a Linux virtual machine (eg, Ubuntu) on Windows. The Illumina/GTCtoVCF converter tool is considered semi-archived, and as of May 2023, Illumina recommends using the fully supported DRAGEN Array Local Analysis solution for IDAT-to-GTC-to-VCF conversion.

**PLINK**

This workflow generates VCF files by exporting data from GenomeStudio to PLINK format and then converting the data to VCF using PLINK tools.1. Download the [PLINK Input Report Plug-in v2.1.4](https://support.illumina.com/downloads/genomestudio-2-0-plug-ins.html) from the GenomeStudio 2.0 Software Downloads page.\
2\. Open the GenomeStudio 2.0 project.\
3\. Navigate to Analysis > Reports > Report Wizard.\
4\. Select Custom Report and choose PLINK Input Report from dropdown menu.\
5\. Export the PLINK report in PED file format.\
6\. Import the PED file into PLINK to generate VCF file. Conversion to VCF can be performed using [PLINK/SEQ.](https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fatgu.mgh.harvard.edu%2Fplinkseq%2F)

**Note:** The PLINK Input Report plug-in is not directly supported by Illumina. For further support, users should reach out to PLINK developers directly.

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                   |
| :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #3079), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006686%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000003079.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.