Illumina Support
The following will help make the integration with Illumina as seamless as possible:
HelixTree DSF Export Plug-in for BeadStudio
In collaboration with Illumina, Golden Helix has developed a set of custom plug-ins that streamline the transfer of genotype, copy number and bookmark files between Golden Helix's SNP & Variation Suite applications and Illumina's BeadStudio Data Analysis software.
Note: You will need BeadStudio 3.0 or greater to access the plug-ins. If you have an earlier version of BeadStudio you can use the final report feature to export genotype data into a text file format, which can then be imported in HelixTree using an import script (copy number and bookmark data are not supported).
See Appendix D.3 of the HelixTree Manual for more detailed Illumina export/import information.
For 32 bit installations of BeadStudio
Before beginning the installation, make sure all instances of BeadStudio are not running.To install the HelixTree Plug-in into Illumina BeadStudio, you must first download the following plug-in installer:
HelixTreeBeadStudioPlugin.exe
When the download has completed, open the installer and click Next to continue the installation. The second window will ask for a directory to extract the plug-in to; by default, the location is the standard BeadStudio installation directory:
C:\Program Files\Illumina\BeadStudio 2.0
Click Next and the installation will be finished. Three plug-ins will be made available with this installation: a DSF export plugin for exporting SNP call data or copy number LogR ratios, an import bookmark file plug-in that allows you to view copy number segmenting results generated in HelixTree, and a segment means import plug-in that allows you to view copy number segment means data calculated in HelixTree.
For more information see Appendix D.3 of the HelixTree Manual.
For 64 bit installations of BeadStudio:
If you have BeadStudio installed on a 64 bit machine you will need the following plug-in:
HelixTree_x64Beadstudio_Report_Plugin.zip
Unzip the files to the C:\Program Files (x86)\Illumina\BeadStudio 2.0\Modules\BSGT\ReportPlugins folder.
Creating Illumina Marker Maps from BeadStudio
Check out the following knowledge base article to learn how to create Illumina marker maps using BeadStudio.
