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Illumina

3.9 Illumina

Four different Illumina file types can be imported via the Illumina submenu of the import menu. These include Illumina DSF File, Illumina Final Report, Matrix Text File, and iControlDB Data.

Illumina DSF File

For the Illumina platform, you must use BeadStudio or GenomeStudio with the SVS DSF Plug-In to export the log2 ratio values from your Bead/GenomeStudio project. For instructions on how to install and use the plug-in see Exporting Data from GenomeStudio. With the DSF Plug-In, you can choose to export the entire project or specific chromosomes.

The Import Illumina DSF File dialog allows you to directly import log2 ratio data into a spreadsheet. This process will import all of the chromosomes stored in the DSF file.

Illumina Final Report

This option imports multiple fields of data from Illumina Final Report text files. It can be used to just import genotype data, or multiple real- valued columns such as B-Allele Frequency, or Log R Ratios. The user can choose from all fields found in the text file and select which ones should be imported.

A separate dataset is created for each field, except for allele fields which are combined into a genotype column and GC score which is used to filter genotypes.

Illumina Matrix Text File

The option imports a user-specified file in the matrix Illumina text format that can be exported using the Final Report wizard in Illumina’s BeadStudio Software. The file can be comma or tab delimited amd GC calls can either be included or excluded.

The exported file will contain file information, a header line and then the genotype data.

During the import process, you will be prompted to choose a file to import. Once chosen you will be asked to specify whether your file is tab or comma delimited, and if the file contains GC Score data. If you choose to use a GC Score threshold, a second dialog box will appear asking you to to input your threshold value (range: 0 - 1). SNPs that have a GC Score below this threshold will be imported as missings (?_?).

The SNPs will be saved in the spreadsheet in the order they appear. You will still want to import a marker map and apply it to get a reordered spreadsheet.

Illumina iControlDB Data

This options imports iControlDB formatted data into SVS. Illumina’s iControlDB is an online database containing publicly available data, to be used as controls, for example, in an association study. The data will contain genotype and phenotype data from individuals generated from Illumina genotyping products.