Patient tab, Variants sub-tab context menu
You can right-click a variant on the Variants sub-tab to open a context menu with the following options:
Option | Description |
|---|---|
Variant Details | Opens the Variant tab for the selected variant. See Overview of the Variant Tab. Note: You can also double-click the variant to open the Variant tab. |
Show Variants Filtered by Panel | Displays all the variants in all the associated samples for the selected patient filtered by a selected panel or panels. If you select this option, then the Select Panel to Filter Variants dialog box opens. You must select a panel or panels in this dialog box by which to filter the variants for the selected patient. |
Show Samples with Selected Variants | |
All Variants | Select a variant, or CTRL-click to select multiple variants and then select this option to open the Samples with all variants pane, which displays a list of all the samples in your Geneticist Assistant database that contain all the selected variants. You can right-click a sample in the list to open a context menu with sample-specific options. See The Samples Pane (Run tab) Context Menu. |
Any Variants | Select a variant, or CTRL-click to select multiple variants and then select this option to open the Samples with all variants pane, which displays a list of all the samples in your Geneticist Assistant database that contain one or more of the selected variants. You can right-click a sample in the list to open a context menu with sample-specific options. See The Samples Pane (Run tab) Context Menu. |
Edit Variant - Contains all the sub-menu options for editing and deleting a variant. | |
Add Variant Comment | Opens the Add Variant Comment dialog box. You can add a comment for a selected variant in the Add Comment field, and then click OK. You can also CTRL-click to select multiple variants and add the same comment to all the selected variants in a single step. The comment is displayed in the Variant Comment field in the Variants pane on the Search Results tab, the Variant Comment field on the Variants sub-tab on the Patient tab, the Sample Variant Data sub-tab on the Sample tab, the Variant Comment field in the Variant pane on the Variant tab, and the Variant Comments pane on the Variant tab. Note: If multiple comments have been added for a variant, then with the exception of the Variant Comments pane on the Variant tab, only the last added comment is displayed in all the locations that are detailed above. All the comments that have been added for a variant, including the last added, are displayed in reverse chronological order in the Variant Comments pane on the Variant tab. |
<Add Variant Interpretation> | Select a variant, or CTRL-click to select multiple variants. • If a single variant is selected, then the option is Add Single Variant Interpretation, and the Add Single Variant Interpretation dialog box opens. • If two or more variants are selected, then the option is Add Compound Variant Interpretation and the Add Compound Variant Interpretation dialog box opens. |
Update Pathogenicity | The pathogenicity of the variant, which is the potential for the variant to cause disease. By default, the pathogenicity is always set to an initial value of Unassigned. You must review the information for the variant and then decide what the pathogenicity should be; for example, Deleterious. (If you cannot determine the pathogenicity of the variant, then you can set the status to Unknown.) When you update the pathogenicity and/or status, you can apply the changes to: • the panel group - Applies the changes to the variant for the indicated panel group.The next time that the variant is detected in another sample that has been assigned to this panel group, then this is the pathogenicity that is displayed for the variant. • the sample only - Applies the changes to the variant only for the currently selected sample. You can also update the pathogenicity status and/or add comments for the changes. By default, the status is always set to an initial value of Pending. Note: You can also double-click in the Pathogenicity column to open the Submit Pathogenicity dialog box. The following information is relevant to updating the pathogenicity and/or pathogenicity status for a variant: • By default, only five pathogenicities—Deleterious, Likely Deleterious, Unknown, Likely Benign, and Benign—are available. You have the option of adding custom pathogenicities, either by clicking New to open the Add New Pathogenicity dialog box and entering a new value, or from the Manage Objects function. See Managing Objects in the Geneticist Assistant Database. • By default, only two statuses—Pending and Confirmed—are available. You have the option of adding custom statuses, either by clicking New to open the Add New Pathogenicity Status dialog box and entering a new value, or from the Manage Objects function. See Managing Objects in the Geneticist Assistant Database. • Optionally, you can add supporting information for this pathogenicity change. See To add supporting information for a variant. • You always have the option of updating just the pathogenicity status for a variant. See Update Pathogenicity Status. • You can also update the pathogenicity on the Sample tab, Sample Variant Data sub-tab. See Sample Variant Data Sub-Tab. |
Update Pathogenicity Status | Select a variant, or CTRL-click to select multiple variants and then select this option to open the Submit Pathogenicity Status dialog box. You can update the pathogenicity status for the selected variants in this dialog box. When you update the pathogenicity status, you can apply the changes to: • the panel group - Applies the changes to the variant for the indicated panel group. The next time that the variant is detected in another sample that has been assigned to this panel group, then this is the pathogenicity status that is displayed for the variant. • the sample only - Applies the changes to the variant only for the currently selected sample. • You can also add a comment for the status change. By default, the pathogenicity status is always set to an initial value of Pending. You must review the information for the variant and then decide what the pathogenicity status should be. By default, only two statuses—Pending and Confirmed—are available. You have the option of adding custom statuses, either by clicking New to open the Add New Pathogenicity Status dialog box and entering a new value, or from the Manage Objects function. See Managing Objects in the Geneticist Assistant Database. The following information is relevant to updating the pathogenicity status for a variant: • You can also double-click in the Pathogenicity Status column to open the Update Variant Pathogenicity Status dialog box. • You can also update the Pathogenicity Status for a variant on the Sample tab, Variant Data sub-tab. See Sample Variant Data Sub-Tab. |
Update Artifact Type | Select a variant, or CTRL-click to select multiple variants and then select this option to open the Update Artifact Type dialog box. You specify the artifact type (for example, Sequencing) for the variant in this dialog box. When you specify the artifact type, you can set the artifact type as the following: • Set globally—Set this artifact type for the variant, regardless of the sample in which the variant is detected. • Set for Sample—Set this artifact type for this variant only for the indicated sample. You also have the option of adding comments for the variant artifact type. Note: The default value for Variant Classification is determined by the setting on the Variant Preferences tab on the Settings dialog box. See To specify variant preferences. You have the option of adding custom artifact types, either by clicking New to open the Add New Artifact dialog box and entering a new value, or from the Manage Objects function. See Managing Objects in the Geneticist Assistant Database. Note: You can also define artifact types and set the artifact type for a variant in the Variants pane, on the Variants sub-tab on the Panel Statistics tab from the Runs tab or the Run tab, or on the Sample Variant Data sub-tab on the Sample tab. |
Update Preferred Transcript | Opens the Set Preferred Gene/Transcript dialog box. You can select a different preferred gene and/or transcript for the variant. When you select a different gene/preferred transcript, you can set the preferences for one of the following: • globally - for all panels and panel groups. • of panel - for only the indicated panel. • of Variant - only for this particular variant and not for any other positions within this panel or panel group. Note: When you select a different transcript here for a panel, then the preferred transcript that is used for a gene or genes is permanently changed for the panel. You can also permanently change the preferred transcript by adding a preferred transcript list for the panel. See To set or delete a preferred transcript list for a panel. To temporarily change the preferred transcript for a gene or genes, you simply select the transcript on the Transcript dropdown list on a tab or sub-tab. |
Delete Variant from This Patient | Deletes the selected variant from all samples for the selected patient in which it was found. |
Delete Variant from All Samples | Deletes the selected variant from all samples in which it was found. |
External - Contains all the sub-menu options for viewing the sample variants in a tool that is outside Geneticist Assistant. | |
View in IGV | Opens the variant for viewing in the Integrated Genomics Viewer. Note: To view a variant in IGV, your IGV settings must be specified. See To specify the IGV settings. |
View in Alamut | Opens the variant for viewing in Alamut. Note: To view a variant in Alamut, your Alamut settings must be specified. See To specify third-party (Alamut, IGV, OMIM) settings. |
View in UCSC | Opens the variant for viewing in the UCSC Genome Browser. |
View PubMed Abstract | Searches PubMed for the variant and displays the appropriate abstract in the PubMed Abstract window. You can do the following for the abstract: • In the Link field, enter a different PubMed URL, and then click the Go To icon  to navigate to abstract.• Click Save As to save the abstract as a PDF with a name and in a location of your choosing. • Click Print to print the abstract. |
Export - Contains all the sub-menu options for exporting a variant. | |
Export Selected Variants to VCF | Exports the selected variants to a VCF file. CTRL-click to select multiple variants. You must specify both the file name and the location in which to save the file. |
Export All Variants to VCF | Exports all the variants to a VCF file. You must specify both the file name and the location in which to save the file. |
Reports - Contains all the sub-menu options for generating a report that includes the variant. | |
Add Selected Variants to Custom Report | Selects all the data that is displayed for the selected variant for inclusion in a custom report. CTRL-click to select multiple variants. See Geneticist Assistant Reports. |
Add All Variants to Custom Report | Selects all data that is displayed for all the variants for inclusion in a custom report. See Geneticist Assistant Reports. |
Copy | Copies the information for the selected variant to your client’s clipboard. You can use standard Paste commands to paste the copied information in to a third-party application such as Notepad. |
Create Variant Filter from Selected Variants | Create a filter based on the selected variants. You can select a single variant, or CTRL-click to select multiple variants to open the Create Variant Filter dialog box. Name the filter and indicate if the filter is to be available to all users. You, and if applicable, other users can use the Load Filter Template function to apply this variant filter to a selected sample or samples. (See To load a saved filter template.) When the Sample tab opens for a sample to which the filter has been applied, then the Sample Variant Data sub-tab displays only those variants that meet the filter criteria. |
Load Columns | |
Manually | Opens the Select Columns dialog box in which you can select columns that are to be shown and clear the columns that are to be hidden dynamically, or select a configuration from the list of available column configurations. This option is also available on the column header context menu for the sub-tab. Note: For information about showing and hiding columns dynamically, see To show/hide columns in a tab pane. Note: If you set column display preferences here, then you can display preferences for variants in all the variant sub-tabs and panes (with the exception of the Sample Group columns on the Sample Variant Data sub-tab on the Sample tab and the Variant pane on the Variant tab) in a single step. See To apply shared preferences or to clear all tab preferences. |
Compact | Displays the data columns on the sub-tab in a more condensed view. To toggle the display, click Compact as needed. |
<Saved Pane Configuration Name> - Saved by <User Name> | Publicly available pane configurations. The name of the user who created a pane configuration is displayed next to the configuration name. |
Load Filters | |
Manually | Opens the Filters table for the Variants pane. See To filter the data that is displayed in a tab pane. |
<Filter Template Name> - Saved by <User Name> | Opens the saved Filter template for the Variants pane. Limits the display in the pane to only the data (fields) that are defined by the template. See To filter the data that is displayed in a tab pane. |