Option | Description |
|---|---|
Run | • Open – Opens the Run tab for the selected run. See Geneticist Assistant Data Review - Run Tab. Note: You can also double-click a run entry to open the Run tab. • Open all Samples with <Filter>: Select a filter for the samples. One or more Sample tabs open. The Sample Variant Data sub-tab is the open tab and the selected filter is applied to each tab. For each sample, 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 samples, or to permanently clear the filter for the samples, 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. |
Show Run Variants | Displayed for one or more runs. CTRL-click to select multiple runs. You can select only one of the four options. All options open the Sample Variant Data sub-tab for the Sample tab, which displays variants for one or more samples. |
• All | • Displays all the variants for all the samples in all the selected runs. |
• Distinct | • Displays all the variants that are different among all the samples in all the selected runs. |
• All Filtered by Panel | • Displays all the variants among all the samples in all the selected runs 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. |
Add All to Custom Report | Selects all the data that is displayed for the run for inclusion in a custom report. See Geneticist Assistant Reports. |
Compare Samples | Applicable only for runs with two or more samples. 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. |
Panel Statistics | Opens the Panel Statistics tab. The tab has options for displaying specific information based on the panel that was used for the run. See Reviewing Panel Statistics. |
Copy | Copies all the information that is displayed for the selected run 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 run. See Setting Read and Write Permissions. |
Change Ownership | Opens the Change Run Ownership dialog box, which displays the name of the current owner for the run, and an option (New Owner) for selecting a new owner for the run from a list of all the currently available and active users for your Geneticist Assistant instance.You can change the ownership for any run if you are an Administrator user, the current owner of the run, or if you have been granted Can Read and Can Write permissions for the run. Note: If the run was added to your Geneticist Assistant prior to V1.4, then the first time the dialog box opens, the Current Owner field is blank. |
Edit Run | |
Apply Variant Filter | • <Filter>: Applies the selected variant filter to all the samples in the run. When you open the Sample tab for any sample in the run, the variant filter is automatically applied. Only those sample variants that meet the filter criteria are displayed on the Sample Variant Data sub-tab of the Sample 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 filters that been applied for all the samples in the run for all instances of Geneticist Assistant. All variants for a selected sample are again displayed on the Sample Variant Data sub-tab. |
Add Comment | Opens the Add Run Comment dialog box. You add a comment for the selected run in the Add comment field. The comment is displayed in the Comment field on the Runs tab and the Comment field in the Comments pane on the Run tab. Note: If multiple comments have been added for a run, then only the last added comment is displayed in the Comment field on the Runs tab. All the comments that have been added for a run, including the last added, are displayed in reverse chronological order in the Comments pane on the Run tab. |
Add Samples to Run | Opens the New Run dialog box so that you can add more samples to the selected run. See Adding a Run. |
Set Subpanels of Selected Runs | Applicable only if you select a run for which a subpanel was not selected during the setup of the run. CTRL-click to select multiple runs. If you select multiple runs, then all the runs must use the same panel. Opens the Select a Subpanel dialog box. The dialog box displays the samples and the panel for the selected runs and a Subpanel dropdown list with all the available subpanels. Select a different subpanel on the Subpanel dropdown list, and then click OK. The subpanel is applied to all the samples in all the selected runs. |
Delete Run | Delete the selected run from the Geneticist Assistant database. |
Export - Contains all the sub-menu options for exporting a variant. | |
Export to VCF | Exports all the variants in the selected run 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 runs. CTRL-click to select multiple runs. Generates an individual sample report for each sample in all the selected runs. 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 all the samples in a selected run. See Managing a Batch Variants Report. |
Create Batch Coverage Report | Opens the Batch Coverage Report dialog box for generating the Batch Coverage report for all the samples in the selected run or runs. See Generating a Batch Coverage Report. |
Sample PDF Report | |
Applicable for one or more runs. CTRL-click to select multiple runs. Opens a list of Sample PDF 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 sample in all selected runs. 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 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 Runs 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 Run 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. |