Mutation Report Settings dialog box

NextGENe Online Help : NextGENe Viewer Reports and Tools : Sequence Alignment Project Mutation Report Settings : Mutation Report Settings dialog box

The Mutation Report Settings dialog box contains the options for the general settings for the Mutation report. To open the Mutation Report Settings dialog box, do one of the following:

• On the NextGENe Viewer main menu, click Reports > Mutation Report > Mutation Report Settings.

• On the NextGENe Viewer toolbar, click the Report Settings icon.

The dialog box contains four primary tabs: the Display tab, the Filter tab, the Summary Report tab, and the Output tab. The Display tab is the open tab when the dialog box opens. You specify the general settings for generating the Mutation report on the tabs and sub-tabs of the Mutation Report settings dialog box.

Tab	Description
Display	The active tab when the Mutation Report Settings dialog box first opens. The settings on the Display sub-tabs determine the numerous columns that can be displayed in the Mutation report based on the information that is required for the project and the information that is included in the reference sequence.
Filter	The settings on the Filter sub-tabs determine what kinds of variants are displayed in the report.
Summary Report	The settings on the Summary Report tab determine how the Mutation report is displayed if it is included in the Summary report.
Output	The settings on the Output tab determine the additional formats (SIFT and VCF) in which the Mutation report can be saved and what type of consensus sequence is to be saved.

When the Mutation Report Settings dialog box is open, you can specify the settings for a new report on the various tabs and sub-tabs of the dialog box, and then click OK to generate the report, or you can click Settings to open a Settings menu, and then do any of the following:

• Click Load from file to browse to and select a Settings file (.ini file) to generate the Mutation report based on the saved settings in the file.

• Click Save to file to save your settings for the report in a Settings file (.ini file). You can use this saved Settings file to generate the Mutation report for another project based on the settings in the file. You can also select this saved general Settings file for post-processing options in:

• The Project Wizard. See To specify the post-processing options for a Sequence Alignment project.

• The NextGENe AutoRun tool. See The NextGENe AutoRun Tool.

• The Summary report. See Summary Report.

• Click Default to return all selections and all values on all tabs and sub-tabs on the Mutation Report Settings dialog box to their default values in a single step.

For a detailed discussion of the options that are available on each tab and sub-tab, see:

Tab	Options
Display	• Display tab, Annotation sub-tab. • Display tab, Statistics sub-tab. • Display tab, Phasing sub-tab. • Display tab, Order sub-tab.
Filter	• Filter tab, Annotation sub-tab. • Filter tab, Bias sub-tab. • Filter tab, Score sub-tab. • Filter tab, Statistics sub-tab. • Filter tab, ROI sub-tab.
Summary Report	Summary Report tab.
Output	Output tab.

The above list details the default tabs and sub-tabs for the Mutation Report Setting dialog box as well as the sub-tabs for the dbNSFP track. Additional sub-tabs are displayed for custom tracks that are imported with the Track Manager.