To create a QC Threshold file for panel regions
After you edit the coverage values for the regions of one panel, you can save these edited values to a QC Threshold text file. You can save this file as record of the QC thresholds that were used for the panel and you can also load this text file to apply these coverage thresholds to a different panel.
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 Panel dropdown list, select the appropriate panel.
c. Click Download and Edit Panel Regions to display the panel regions on 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 also displayed. 2. Manually enter a new value, or click the Up/Down arrows to change the value accordingly. |
3. Click Save QC Threshold File.
The Save File dialog box opens. By default, the QC Threshold file is named as <Panel Name>_qc_threshold, and it is saved in the same directory as the BED file for the panel. The file type is a text file, and you cannot change this.
4. Optionally, change the name for the QC Threshold file, and/or the directory in which to save the file, and then click Save.
5. If you are done with the configuration of the newly added or edited panel, then click OK to close the Manage Panels dialog box and return to the Geneticist Assistant main window. (The edited coverage values are now saved for the panel in the Geneticist Assistant database.) Otherwise, continue to one or both of the following as needed: