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Exporting Data using the SVS DSF Export 4.0 Plug-In

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19.3 Exporting Data using the SVS DSF Export 4.0 Plug-In

This section will instruct you on how to download and install the SVS DSF Export 4.0 Plug-In to be used with Illumina® BeadStudio or GenomeStudio. You will also be guided through the export of your data from GenomeStudio into Golden Helix, Inc.s proprietary sparse data storage format (DSF) files. Please note, these instructions only apply for BeadStudio version 3.0 or greater or for GenomeStudio. The directions will only refer to GenomeStudio, but the same steps also apply to BeadStudio. A brief discussion on how to import the data into SVS will also be provided.

Installation of the Golden Helix, Inc. Plug-In

Before beginning the installation, make sure there are no instances of GenomeStudio running.

To install the SVS DSF Plug-in into Illumina® GenomeStudio, you must first download the appropriate plug-in installer from http://www.goldenhelix.com/Support/illumina_support.html.

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 GenomeStudio installation directory, for example: c:/Program Files/Illumina/GenomeStudio.

Click Next and the installation will be finished.

Exporting DSF Data from GenomeStudio using Plugin version 4.0

The GenomeStudio Report Wizard

To export a SVS DSF, a GenomeStudio project must be open. From GenomeStudio, open the report wizard by selecting Analysis > Reports > Report Wizard.

From the Report Wizard, select Custom Report and, from the drop down menu, select SVS DSF Export 4.0 from Golden Helix, Inc.. Click Next.

If you have excluded samples inside the GenomeStudio project you will be asked how to handle these excluded samples. The options are to include all of the samples from the report or to only include the selected samples.

Select the sample groups that you wish to include in your report and click Next.

The following window may appear if you have applied filters to your data. Select whether or not you want to include the hidden SNPs in your report, and click Next to continue through the wizard.

Select the Output Path and a Report Name. These parameters will determine the final base file name for all the DSF files created and directory location. Click Finish.

The SVS DSF Export Window

After going through the Report Wizard, a progress bar will appear. After a brief moment, the SVS DSF Export window will open. In this window you must select the output options that determine what type of data you wish to export in DSF format.

The chromosomes to include or exclude from the DSF files can be selected by clicking on Pick Chromosomes. Only chromosomes initially included in the report will be available in the Chromosome Picker.

Information about the selected samples is displayed in the Selected Samples box. If the information in this box does not appear to be correct, cancel the export and adjust the selected samples in the GenomeStudio project. A DSF is automatically created for the samples to export the gender information.

There are six optional DSF output options to choose from:

  • SNPs for Genotype Analysis
  • Log R Ratios for Copy Number Analysis Module
  • B-Allele Frequency
  • Computed CNV Values
  • X/Y Value Pairs for QC
  • X/Y Raw Value Pairs for QC

Any one or all of these DSF files can be exported. These optional files will export data in the optimal export format with samples as columns and markers as rows.

The Output File Name Base is displayed at the bottom of the window. The file name is set by the output directory chosen in the GenomeStudio Report Wizard and can not be changed in this window.

Click OK in the Golden Helix, Inc. DSF Export window to begin the export.

Importing the DSF files into SVS

To import the DSF files into SVS, go to Import > Illumina DSF.

The data will be imported in the format where samples are columns and markers are rows for all files, except the Samples DSF file. The sample gender file has samples in rows and one column of gender information. Some quality control measures can be performed on log ratio data in this orientation, but most analysis requires that markers be in columns and samples be in rows. This requires transposing the data. See Transposing Spreadsheets for help transposing the data.

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