Sample Variant Data sub-tab context menu
You can right-click any column header on the Sample Variant Data sub-tab to open a context menu that, in addition to the standard column header context menu options, contains a Manage Sample Group Statistics Columns option. This option opens the Select Sample Groups dialog box.
• If you used sample groups for a run, then you can indicate the date range for which to calculate statistics based on the added samples.
• If you did not use specific sample groups for a run, then do not select these sample groups, or if applicable, clear the selections for these groups, which hides the corresponding Sample Group Statistics columns from the sub-tab display.
You can also right-click a variant in the Variants pane on the sub-tab to open a context menu with the following options:
Option | Description |
|---|---|
Variant Details | Opens the Variant tab, which displays detailed information about the variant. See Geneticist Assistant Data Review - Variant Tab. |
Show Variants Filtered by Panel | Displays all the variants in the selected sample 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 run. |
Show Samples with Selected Variants | Applicable for one or more variants. CTRL-click to select multiple variants. Two options available: • All variants - Opens 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 variant - Opens the Samples with any variants pane, which displays a list of all the samples in your Geneticist Assistant database that contain any 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 the 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 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 variables 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 Pathogenicity Status. • You can also update the pathogenicity on the Patient tab, Variants sub-tab. See Patient tab, Variants sub-tab. |
Update Pathogenicity Status | Select a variant, or CTRL-click to select multiple variants and then select this option to open the Submit Variant 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. 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 Patient tab, Variants sub-tab. See Patient tab, Variants sub-tab. |
Update Artifact Type | The artifact type for the selected variant. You must manually set this value. Double-click in this column for the selected variant to open the Update Artifact Type dialog box. You specify the artifact type (for example, Sequencing) for the variant in this dialog box. If the appropriate artifact type is not available, then an option is provided to create a new type. When you specify the artifact type, you can set the artifact type as the following: • Set globally—Selected by default. 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. The following information is relevant to updating the artifact type for a variant: • You can also define artifact types and set the artifact type for a variant on the Variants sub-tab on the Patient tab, 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. • 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. |
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 the variant in all panels and panel groups. • of panel - for the variant only when in 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 Sample | Deletes the selected variant from this sample only. |
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 NextGENe | Requires you to have your NextGENe installation specified in your Geneticist Assistant settings. (See To configure Geneticist Assistant directories.) If selected, then Geneticist Assistant browses for the folder where the VCF file for the sample is located. If the NextGENe project file is found in the same directory as the VCF file, then the NextGENe project is opened in the NextGENe Viewer, with the focus set to the position for the selected variant. |
View in IGV | Applicable if there is a corresponding BAM file (and not a NextGENe project file) in the same folder as the VCF file for the sample. Opens the BAM file in the third-party Integrative Genomics Viewer (IGV) with the focus set to the selected variant. |
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 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 Action List | Adds the selected variant to an Action List. CTRL-click to select multiple variants. See Creating an Action List. |
Add Selected Variants to Custom Report | Selects all the data that is displayed for the selected variants for inclusion in a custom report. CTRL-click to select multiple variants. See Geneticist Assistant Reports. |
Add All Variants to Custom Report | Selects all the data that is displayed for all the variants for inclusion in a custom report. See Geneticist Assistant Reports. |
Copy | Copies all the information that is displayed for the selected variant to your client’s clipboard. You can use standard Paste commands to paste this copied information into a third-party application such as Notepad. |
Create Variant Filters 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 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. |
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. |