To import the variants’ pathogenicities, pathogenicity statuses, comments, and/or artifact types
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. Leave Import from VCF’s INFO fields selected.
3. Do either or both of the following:
• If the VCF file contains the pathogenicity and pathogenicity status for each variant, then to import this information, leave the Pathogenicity and Pathogenicity Status option selected; otherwise, if the VCF file does not contain this information, or you do not want to import this information, then clear this option.
• If the VCF file contains comments for the variants, then to import this information, leave the Variant Comment option selected; otherwise, if the VCF file does not contain this information, or you do not want to import this information, then clear this option.
• If the VCF file contains the artifact types for the variants, then to import this information, select this option; otherwise, if the VCF file does not contain this information, or you do not want import this information, then leave this option cleared.
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 will now be displayed with the imported information (such as the pathogenicity) in any samples that contain these variants.