To manually set new coverage thresholds for panel regions
After you have imported a new panel, the coverage values that are initially displayed for each panel region are the global values that are defined on the Quality Control tab of the Settings dialog box. If needed, you can edit these values and save the values for the panel in the Geneticist Assistant database. You can edit the values for all the regions in a single step, or you can set different coverage thresholds on a per region basis.
1. If you have just imported a new panel, then the Manage Panels dialog box is already open and the panel regions are displayed; otherwise, do the following:
a. On the Geneticist Assistant main menu, click Panels > Manage Panels to open the Manage Panels dialog box.
b. On the Select Existing Panel dropdown list, select the appropriate panel.
c. Click Download and Edit Panel Regions to display the panel regions in the bottom pane of the Manage Panels dialog box.
2. Do one of the following:
Action | Steps |
|---|
To edit the values for all regions in a single step | 1. Click Update QC Threshold. The Update QC Threshold for All Regions dialog box opens. 2. For each coverage value that you are editing, double-click it to select it, and then manually enter a new value, or click the Up/Down arrows to change the value accordingly. 3. Click OK. |
To edit the values on a per region basis | 1. Double-click in the appropriate coverage field for a region. The coverage value is selected, and Up/Down arrows are displayed. 2. Manually enter a new value, or click the Up/Down arrows to change the value accordingly. |
3. If you are done with the configuration of the newly added panel, then click OK to close the Manage Panels dialog box and return to the Geneticist Assistant main window. Otherwise, continue to any of the following: