Which files are required and optional when creating a GenomeStudio project?

Required files for creating a GenomeStudio project:

• Red and green intensity data (*.idat) files for each sample; are contained in scan folders with barcode names.

• Manifest file (*.bpm) containing Bead IDs and Single Nucleotide Polymorphism (SNP) information for each marker on the array.

  • A commercial BeadChip manifest can be downloaded from the product-specific Illumina Support page under Product Files.

  • A consortium/custom BeadChip manifest can be downloaded from MyIllumina using a custom product file search.

• For methylation projects, the Sentrix data file (*.sdf) inside the scan folder is required.

Optional files for creating a GenomeStudio project:

• Cluster file (*.egt) containing expected cluster positions for each marker on the array.

  • A commercial BeadChip cluster file can be downloaded from the product-specific Illumina Support page under Product Files.

  • A consortium/custom BeadChip cluster file is not available on the website and must be generated using GenomeStudio.

• Sample sheet (*.csv) containing user-specified sample information.

• A sample sheet template can be downloaded from the product-specific Illumina Support page under Support Files.

• For methylation projects, a cluster file is not used.

Summary Table

File type	Genotyping GenomeStudio 2.0	Methylation GenomeStudio 2011
Intensity data files (*.idat)	Required	Required
Manifest file (*.bpm)	Required	Required
Cluster file (*.egt)	Optional	Not used
Sample sheet (*.csv)	Optional	Optional
Sentrix data file (*.sdf)	Not used	Required

For any feedback or questions regarding this article (Illumina Knowledge Article #2888), contact Illumina Technical Support [e-mail].