‹‹ Back to SVS Home
Exporting Genotype Data using the Final Report
19.2 Exporting Genotype Data using the Final Report
This section will guide you through the export of your genotype data from Illumina® GenomeStudio into the Final Report
text format and then the import of that data in to SVS using the Illumina BeadStudio Final Report by SNP
script.
Exporting the Data from GenomeStudio
Begin by opening a GenomeStudio Project. In the GenomeStudio window select from the menu bar Analysis > Reports
>Report Wizard.
Select in the Report Wizard Final Report and click Next.
Select the sample groups to be included in the report and click Next. Indicate if zeroed SNPs should be included in the report or not and click Next. The next screen will ask you how you would like to format your final report. The options to select are:
- Standard output format
- Displayed Fields in this order:
- SNP Name
- Sample ID
- Allele1 - Top (This can be replaced by any of the other Allele1 options).
- Allele2 - Top (This can be replaced by any of the other Allele2 options as long as it is the same type as the Allele1 selection).
- GC Score
- Group by SNP
- Tab or Comma delimited
- Create map files
When you are finished selecting the proper parameters, click Next.
Select the output path and file name and click Finish.
Importing Data into SVS
To import the Final Report text file into SVS, first open a project in SVS. From the Project Navigator Window select
Import > Import Scripts > Illumina BeadStudio Final Report by SNP.
Select the Final Report file that you exported from GenomeStudio and click Open. A dialog box will appear
asking for the file type, and whether you want to use a GC Score. Using the GC Score will convert genotype
calls into missing values if they do not meet a user-specified threshold. Choose your parameters and click
OK.
If you chose to use a GC Score threshold, a second dialog box will appear asking you to enter that threshold. Input your
GC Score threshold and click OK.
Your data will then be imported into the current project. Once the import is complete, a message will appear with some import statistics recorded in the Annotation Window within the Project Navigator Window.