GMT Tutorial Exercise 21 - Workflow 1 - Step 16

Export the GeneMapper marker data table

• The pre-scored marker data has to be exported from GeneMapper to be analysed for polymorphisms by the Automated Designer for Whole Genome Scan.

1. Ensure that all the alleles are going to be included in the exported GeneMapper table:
   1. Open the Table Settings Editor window (see below) by clicking on the Table Settings Editor button: ,
      or in the following way:
      1. Select Tools » GeneMapper Manager from the main menu, the GeneMapper Manager dialog box opens.
      2. Click on the Table Settings tab.
      3. Double click on the name of the table setting used to view your project, e.g. "Microsatellite Default".
   2. Select the Genotypes tab (shown below).
   3. Ensure that the Show only binned alleles in their respective bin position option (circled in green in the screenshot) is NOT selected.
   4. Click OK to close the Table Settings Editor window.
      If the GeneMapper Manager dialog box is still open, click Done.
   







2. Create a report table in GeneMapper (this step is only necessary once):
   1. Select Tools » GeneMapper Manager from the file menu of the GeneMapper window. The GeneMapper Manager dialogue box will appear.
   2. Click on the Report Settings tab, and select the New button at the bottom left of the GeneMapper Manager dialogue box. The Report Setttings Editor dialogue box opens.
      
   3. Enter a name for the report table in the Name box, e.g. "Report Table for Marker Screening".
   4. Click on the Genotype tab in the Available Columns box and transfer the following table columns to the Selected Columns box (observing the following order):
      • Sample File
      • Sample Name
      • Panel
      • Marker
      • Dye
      • Allele 1
      • Size 1
      • Allele 2
      • Size 2
   5. Click OK to save the report table. The Report Settings Editor dialogue box will close.
   6. Click the Done box to close the GeneMapper Manager dialogue box.




3. In the Genotypes tab of the GeneMapper window, select all the genotype data to be included in the report (use Crtl+A to select all).
4. Select Analysis » Report Manager from the file menu of the GeneMapper window. The Report Manager window opens.
5. From the Report Setting drop-down box, select the report table that was created following the instructions for step (2) above.
   
6. Select File » Export from the file menu of the Report Manager window.
7. Save the report table in the directory folder that was specifically created for the project and that contains the Automated Designer for Marker Screening macro.
   Note:
   By default, GeneMapper creates a file name for the exported report table that is a combination of the GeneMapper "project name" (as entered previously) and the name of the report table created in step (2) above.
8. Select File » Exit from the file menu to close the Report Manager window.