Important file types for analysis of BeadArray data in BlueFuse Multi

BlueFuse Multi uses different file types throughout installation, experiment import, and downstream data processing, each serving a specific purpose within the workflow.

Illumina scanning platforms such as the iScan and the NextSeq 550 generate Infinium BeadArray data (raw image and intensity data files- IDATs) that are required for downstream analysis in BlueFuse Multi. Compatibility of specific BeadChip types with the NextSeq 550 system varies. Refer to the Illumina Knowledge article “Which Infinium BeadChip types can be scanned using the NextSeq 550?” for detailed guidance.

A critical component of the BlueFuse Multi workflow is the annotation database, which must be installed and made available within the software environment. The annotation database contains probe-level information, genomic positions, and content-specific details required to interpret array data accurately. BlueFuse Multi integrates the raw data files with the annotation database to perform normalization, feature extraction, and result generation.

Table 1. Install File Types in BlueFuse Multi

File Type	Description	File Extension
Brf	- BlueFuse Registration File obtained from Illumina Technical Support - Required to register the copy of the software for versions 4.4 and below	.brf
Annotation database	- Contains information about the human genome to aid in the interpretation of experimental results. - Includes the position of genes, exons and publicly available data on CNV frequency shown in the DecisionTrack pane within BlueFuse Multi. - Uses information from major public databases such as ENSEMBL for gene annotation, OMIM for inherited diseases, and DGV and dbVAR for genetic healthy or disease variants. - Lists products eligible for analysis under the particular Annotation database. Products not listed cannot apply the Annotation database for analysis - Used by BlueFuse Multi during analysis and visualization of experiments	.db

Table 2. BeadArray-Specific File Types used with CytoChip Module

File Type	Description	File Extension
GTC	- Genotype call file that incorporates fluorescent image file information - iScan software can be configured to create GTC file automatically as part of scanning or user may use Beeline software to convert IDATs to GTCs. - BlueFuse Multi can automatically extract information from the GTC file name to identify the type of array, the barcode and specific subarray location on the slide, and assign the correct settings	.gtc
SNP Manifest File	- Contains SNP probe information - Specific for each BeadArray type - After a SNP Manifest file is imported and used within a BlueFuse Multi database, it is stored directly in that database.	.bpm
SNP Cluster File	- Provides reference information used in the analysis of the BeadArray - After a SNP Cluster file is imported and used within a BlueFuse Multi database, it is stored directly in that database. The stored cluster file is managed by BlueFuse Multi and is accessed automatically during genotype calling and downstream analysis as required.	.egt

Additional resources:

• BlueFuse Multi Software Guide

• BlueFuse Multi Annotation Database

• Illumina Knowledge Using Beeline to regenerate GTC files with an alternate cluster file or manifest file

• Illumina Knowledge How to generate VCF files from Illumina BeadArray data

For any feedback or questions regarding this article (Illumina Knowledge Article #5043), contact Illumina Technical Support [e-mail].