To export the output to Geneticist Assistant
For Output to Geneticist Assistant to be enabled, User Management must be turned on for your NextGENe instance and you must be logged in appropriately. See To turn on user management. Also, the path for the Geneticist Assistant executable must be specified in the NextGENe process options. See Specifying NextGENe Process Options.
1. Select Output to Geneticist Assistant.
Edit details is enabled as are the Run Name and Sample Name fields. By default, the Sample Name is set to the same as that of the first sample file that was loaded for the AutoRun job.
 | When output is exported to Geneticist Assistant, an unfiltered VCF file is automatically produced and exported, even if loaded post-processing options specify both an unfiltered VCF file and a filtered VCF file. |
2. Enter a Run Name and/or edit the Sample Name.
3. Click Edit details.
The Geneticist Assistant Input Settings dialog box opens. The first time that the dialog box opens, all options are blank; otherwise, the settings that were last specified or the settings that are saved for the template that you have selected are displayed.
4. Specify the Geneticist Assistant Run variables.
5. To submit the BAM and VCF output to Geneticist Assistant, select Submit BAM; otherwise, to import only the VCF output, leave this option cleared.
6. Click OK.
The Geneticist Assistant Input Settings dialog box closes. The NextGENe AutoRun Job Editor dialog box remains opens.
7. If you are done with specifying the needed post-processing options, then return to one of the following as appropriate:
Otherwise, continue specifying any other needed post-processing options. See: