To specify variant preferences
Variant preferences determine how the information about variants is displayed on all the variant tabs, sub-tabs, and panes in Geneticist Assistant.
1. On the Geneticist Assistant main menu, click File > Settings.
The Settings dialog box opens. The General tab is the open tab.
2. Open the Variant Preferences tab.
3. Set the variant preferences.
 | If you edit any variant preferences, then at any time, you can click Restore Default Settings to reset all values to their default values in a single step. |
Option | Description |
|---|---|
Zygosity | |
Heterozygosity Upper Bound (%) | Default value is 80. The maximum variant frequency for a variant to be considered heterozygous. |
Heterozygosity Lower Bound (%) | Default value is 20. The minimum variant frequency for a variant to be considered heterozygous. Note: To report low frequency variants, reduce this value. |
Variant Annotation | |
• Use GFF3 file | • The default value. Use the annotation information in the reference files that SoftGenetics provides. |
• Use GTF file | • Use the annotation information in the reference files that ENSEMBL provides. Note: If you select this option, then you must download the correct references files from ENSEMBL and place them in the Reference directory that is defined for your Geneticist Assistant installation. See To configure Geneticist Assistant directories. |
Highlight user-modified fields | Select this option to highlight any field that a user has modified on all the variant tabs and sub-tabs. This same field is not highlighted on the Variant tab. |
Variant Artifact Default | |
• Assign globally | • Sets the default option for assigning an artifact type for a variant to assigning the artifact type for all samples. You can edit this default value when assigning the artifact type. |
• Assign to specific sample | • Sets the default option for assigning an artifact type for a variant to assigning the artifact type only for the specific sample. You can edit this default value when assigning the artifact type. |
Note: The value that you set here determines the default value for Variant Classification on the Update Variant Artifact Type dialog box. See Patient tab, Variants sub-tab context menu, Variant annotation information, and Sample Variant Data sub-tab context menu. | |
Variant Submission | |
Derive AF from GT if AF not found | Not selected by default. Derive allele frequency (AF) from genotype (GT) if allele frequency not found. If the AF is not found for a variant in the VCF file, then its value is derived from the GT, where: • AF = 0.5 if GT = 0/1, 1/0, 0|1. 1|0 • AF = 1 of GT = 1|1 • AF = 0 if GT = 0|0 |
Submit Hotspots | Not selected by default. Any variants that are included in a VCF file that have an allele frequency value = 0 and/or genotype = 0/0 in the file are submitted to the Geneticist Assistant database. |
Show warnings if a variant is not submitted due to missing AF or GT | Selected by default. A warning is displayed in the console if a variant cannot be submitted to the Geneticist Assistant database because the allele frequency (AF) or genotype (GT) is missing for the variant in the VCF file. |
HGVS Nomenclature - Determines which transcript is used for the HGVS nomenclature columns if a gene has multiple transcripts. | |
• Preferred | Selected by default. Show only a single transcript, either the transcript that is selected by default as the preferred transcript or the transcript that is defined as the preferred transcript in a preferred transcript list. See To set or delete a preferred transcript list for a panel. |
• Unique Translation | Show multiple transcripts if the translation varies among the transcripts. |
• Unique Exon region | Show multiple transcripts if the exon regions vary among the transcripts. |
• All | Shows the HGVS nomenclature based on all the transcripts that are included for the gene. |
Hide predicted if known transcripts exist | Selected by default. If known transcripts exist for the gene, then do not include any predicted transcripts in the HGVS columns. |
Use short description for frameshifts |  |
4. If you are done specifying your settings, then click OK to close the Settings dialog box and return to the Geneticist Assistant main window; otherwise, continue to add and/or edit the information on any of the other tabs as needed.