Variation Tracks Settings dialog box
The Variation Tracks Settings dialog box contains the tracks settings for the Mutation report based on the variation databases that were imported for the project. (After being imported into NextGENe, a variation database is referred to as a track.)
You can select what information to display for the tracks and you can filter the variants in the Mutation report based on the tracks.
1. On the NextGENe Viewer toolbar, click the Tracks Settings icon, and then select Variation Tracks Settings.
The Variation Tracks Settings dialog box opens. The Tracks tab is the open tab. The Tracks pane is the left pane for the Tracks tab. The pane displays all the variation databases, or tracks, that are available for the selected project.
2. To remove all the current display and filter settings based on all the tracks, click Load Settings > Clear all tracks, and then click OK; otherwise, go to Step 3.
3. In the Tracks pane, select a track, and then do the following:
a. Indicate the types of variants that are to be included in the Mutation report.
Option | Description |
|---|---|
All | By default, all variants that meet all the filtering criteria are displayed in the Mutation report, whether they are included in the selected track. |
Reported | Select Reported to display only those variants that are included in the selected track |
Unreported | Select Unreported to display only those variants that are not included in the selected track. |
b. Specify the filter settings (At least [ ] Criteria Satisfied) for the track.
 | The track filter settings available depend on the tracks included for the project. Information for filtering based on some example variant tracks is presented in the Variation Track Settings. |
c. Click Report Display to open the Report Display Settings dialog box, and then do the following:
i Optionally, to include the group identification for the track in each column heading, for example, dbNSFP, select Display track group.
ii. Optionally, to include the name for the track as defined when importing the track in the Track Manager in each column heading, select Display track name.
iii. On each tab, select the columns that are to be included in the report, or click Select All to select all columns in a single step.
| | The Report Display Settings dialog box lists all the display settings (columns) that can be included in the Mutation report for the track. The options that are available vary based on the selected track. |
4. Click OK to close the Report Display Settings dialog box.
5. Optionally, to specify the columns and the order in which the are to be displayed in the report, click Order Columns to open the tab, and then do any of the following; otherwise, go to Step 6.
The Order Columns tab lists all the columns that can be selected for the report display. A checkmark indicates if a column is currently selected for display.
• Individually clear the selections for the columns that are not to be displayed or individually select the columns that are to be displayed.
• By default, Hide Unselected Columns is selected. To show all possible columns in the report display (selected and unselected), clear this option; otherwise, only the selected columns are shown in the report display.
• The order of the columns in the Order Column tab is the order that report columns are displayed in the report. To change the order of the column display, click a column to select it, and then drag it to a new location in the column list.
6. Do one of the following to save your settings and close the Variation Tracks Settings dialog box:
Option | Description |
|---|---|
Click OK. | Going forward, the Mutation report is generated according to these saved settings until you change them. |
Click Save Settings > Save User Defaults. | The settings that you have specified for all the tracks are saved as your (the logged in user’s) default settings. Going forward, any new sequence alignment project that you run in NextGENe uses these settings by default. If you change the settings for a project and want to generate the Mutation report based on your default settings, then you can click Load Settings > Load User Defaults to restore your default settings. |
Save Settings > Save To File. | The settings that you have specified for all the tracks are saved to a Settings (.ini) file. Going forward, you can click Load Settings > Load From File to load this saved Settings file and generate the Mutation report according to the settings in the file. |
| | You can also load this saved *.ini file in the post-processing step of the Project Wizard to automatically generate the Mutation Report based on these settings. |