To manually define the variants’ pathogenicities, pathogenicity statuses, comments, and/or artifact types
When you manually define the pathogenicities, statuses, and/or artifact types for the variants, these properties are set to the same values for all the variants in the file. If you add a comment, then the same comment is added for all the variants.
1. If you have not already done so, on the GeneMarker HTS main menu, click Tools > Import Variants to open the Import Variants dialog box.
2. Select the Select Manually option.
The Import Variants dialog box is updated with options for setting the pathogenicity and the pathogenicity status for the variants as well entering a common comment and/or setting the artifact type for the variants.
3. Do any or all of the following:
• On the Pathogenicity dropdown list, select the pathogenicity for the variants.
• On the Pathogenicity Status dropdown list, select the pathogenicity status for the variants.
 | Remember, you have the option of specifying custom pathogenicity types. Also, by default, only two statuses are available—Pending or Confirmed. You have the option of adding custom pathogenicity statuses. See Managing Objects in the Geneticist Assistant Database. |
• In the Pathogenicity Comment field, enter a common comment for all the variants.
• Select Artifact Type, and then on the Artifact Type dropdown list, select a common artifact type for all the variants.
4. Click OK.
The Import Variants dialog box closes. A Current Jobs tab opens that shows the progress of importing the VCF file. The tab remains open after the import is complete. The variants with the selected information are now imported into the Geneticist Assistant database. These variants are now displayed with the specified information (such as the pathogenicity) in any samples that contain these variants.