Option | Description |
|---|---|
Open with <variant filter > | Select a filter for the sample. The Sample tab opens for the selected sample. The Sample Variant Data sub-tab is the open tab and the selected filter is applied to the tab. Only those sample variants that meet the filter criteria are displayed on the tab. The selected filter is persistent within this Geneticist Assistant instance and across instances. To clear the filter only for the current instance of Geneticist Assistant, click Clear at the bottom of the Table Filters pane. To select a different filter for the sample, or to permanently clear the for the sample, see Apply Variant Filter under Edit Sample. Note: For information about creating a filter template, see To filter the data that is displayed in a tab pane. For information about the Sample Variant Data sub-tab, see Sample Variant Data Sub-Tab. |
Sample Details | Displayed only if a single sample is selected. Opens the Sample tab, which contains detailed information about the sample, including the variant list. See Geneticist Assistant Data Review - Sample Tab. |
Show Sample Variants Filtered by Panel | Displayed only if a single sample is selected. 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. |
Coverage Regions | Displayed only if a single sample is selected. Opens the Coverage Regions tab, which lists the coverage information for every region in your panel. The Status indicates whether the region passed or failed the Quality Control (coverage) settings that were set for the run. See Coverage Regions tab. |
Show Sample Variants | Displayed only if two or more samples are selected. You can select only one of the four options. All options open the Sample Variant Data sub-tab for the Sample tab. |
• All | • Displays all the variants for all selected samples. |
• Distinct | • Displays all the variants that are different among the selected samples. |
• All Filtered by Panel | • Displays all the variants for all selected samples filtered by the selected panel. |
• Distinct Filtered by Panel | • Displays all the variants that are different among the selected samples filtered by the selected panel. |
Compare Samples | Displayed only if two or more samples are selected. Opens the Sample Comparison dialog box. You use the options on this dialog box to compare the coverage, frequency, and read balance information for each sample that is being compared. See Comparing Samples in a Run. |
Family Comparison | Displayed only if three or more samples are selected. At a minimum, you must select two parent samples and one child sample. You can always select more than one child sample. Opens the Family Comparison dialog box, in which you can specify the options to compare the variant calls in family (relation and phenotype) data. See To compare family data. |
Panel Statistics | Opens the Panel Statistics tab. The tab has options for displaying specific information for the panel that was used for the run. See Reviewing Panel Statistics. |
Add All to Custom Report | Selects all the data that is displayed for all the samples in the run for inclusion in a custom report. See Geneticist Assistant Reports. |
Copy | Copies all the information that is displayed for the selected sample to your client’s clipboard. You can then use standard Paste commands to paste this copied information into a third-party application such as Notepad. |
Permissions | Opens the Permissions dialog box.You use the options on this dialog box to set or edit the permissions (Can Read or Can Read and Can Write) that the specified users or groups are to have for the sample. See Setting Read and Write Permissions. |
Change Ownership | Opens the Change Sample Ownership dialog box, which displays the name of the current owner for the selected sample, and an option (New Owner) for selecting a new owner for the sample. You can change the ownership for any sample if you are an Administrator user, the current owner of the sample, or if you have been granted Can Read and Can Write permissions for the sample. |
Edit Sample | |
Apply Variant Filter | • <Filter>: Select a variant filter for the sample. The Sample tab opens for the selected sample. The Sample Variant Data sub-tab is the open tab and the selected variant filter is applied to the tab. Only those sample variants that meet the filter criteria are displayed on the tab. The selected filter is persistent within this Geneticist Assistant instance and across instances. To clear the filter only for the current instance of Geneticist Assistant, click Clear at the bottom of the Table Filters pane. • Deactivate Filters: Permanently clears all applied variant filters for the selected sample for all instances of Geneticist Assistant. All variants for the selected sample are again displayed on the Sample Variant Data sub-tab. |
Add Comment | Opens the Add Sample Comment dialog box. You add a comment for the associated sample in the Add Comment field. The comment is displayed in the Comments field on the Samples sub-tab on the Patient tab, the Comments field in the Samples pane on the Run tab, and in the Comments pane on the Sample Data sub-tab on the Sample tab. Note: If multiple comments have been added for a sample, then with the exception of the Comments pane on the Sample Data sub-tab on the Sample tab, only the last added comment is displayed in all the locations detailed above. All the comments that have been added for a sample, including the last added, are displayed in reverse chronological order in the Comments pane on the Sample Data sub-tab for the Sample tab. |
Set Subpanel/Set Subpanel of Selected Samples | Applicable for one or more samples for which a subpanel was not selected during the setup of the run. CTRL-click to select multiple samples. Opens the Select a Subpanel dialog box. The dialog box displays the selected sample or samples, the panel for the currently selected sample, and a Subpanel dropdown list with all the available subpanels. Select a subpanel on the Subpanel dropdown list, and then click OK. The subpanel is applied to sample or samples. |
Set Patient | Opens the Set Patient dialog box. Select the patient that you are associating with the sample, and then click OK. Note: You also have the option of associating a patient with a sample from the Sample tab. See Patient pane (Sample Data sub-tab for the Sample tab). |
Edit Sample Groups | Opens the Edit Sample Group dialog box. You use the options on this dialog box to add a sample to a selected sample group, or to remove a sample from a selected sample group. Note: If the appropriate sample group is not available, you can add it. See Managing Objects in the Geneticist Assistant Database. |
Move Samples to Run | Applicable for one or more samples. CTRL-click to select multiple samples. Opens the Move Selected Samples to Run dialog box. Enter a search string to search for the existing run in your Geneticist Assistant database that you are moving the samples to. As you enter the search string, a dynamically updated list of runs that meet your search criteria opens. You can select the appropriate run from this list. Note: The search string is not case-sensitive, but the string must begin with the run name. For example, a search string of “May” or “ma” returns a run named Mayo Clinic Run II, but a search string of “clinic” does not. |
Delete Sample/Delete Selected Samples | Applicable for one or more samples. CTRL-click to select multiple samples. Deletes the selected samples from the run. The samples are NOT deleted from the Geneticist Assistant database. |
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. |
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). |
Export - Contains all the sub-menu options for exporting a variant. | |
Export to VCF | Exports all the variants in the selected sample to a VCF file. You must specify both the file name and the location in which to save the file. |
Save Sample Reports | Applicable for one or more samples. CTRL-click to select multiple samples. Generates an individual sample report for each selected sample. If a single sample is selected, then a default location, report name, and report type (.csv) are provided, but you can change any or all of these values. If multiple samples are selected, then you can select only the location in which to save the report. Each report is named the same as the sample and the report format is .csv, and you cannot change either of these values. Note: For more information about standard reports, see Geneticist Assistant Reports. |
Create Batch Variants Report | Opens the Batch Variants Report dialog box for generating the Batch Variants report for the selected sample or samples. (CTRL-click to select multiple samples.) See Managing a Batch Variants Report. |
Create Batch Coverage Report | Opens the Batch Coverage Report dialog for generating the Batch Coverage report the selected sample or samples. (CTRL-click to select multiple samples.). See Generating a Batch Coverage Report. |
Reports | |
Add All to Custom Report | Adds only the data that you select to the custom report. You must CTRL-click to select multiple items for inclusion in the report. See Generating a Custom Report. |
Add Selected Samples to Custom Report | Adds all the data that is currently displayed in the pane to the custom report. See Generating a Custom Report. |
Sample PDF Report | |
Applicable for one or more samples. CTRL-click to select multiple samples. Opens a list of custom report templates that you created and saved, or that other users created and made available to all users. Select a report template to generate an individual sample report for each selected sample. Each sample report is saved in a PDF format and is named the same as the sample for which it was generated. See Designing a Sample PDF Report Template and Generating a Sample PDF Report. | |
Load Filter | |
Manually | Opens the Filters table for the Samples 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 Samples 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. |