You can change many user interface and track settings in the Preferences window, accessed from the View menu. Most setting changes are applied immediately, but some will require an IGV restart.
The preferences are stored in the
prefs.properties file in the
igv directory, normally located in the user home directory.
Resetting to default values
To restore IGV's default preferences, first shut down IGV, then delete the prefs.properties file, or rename it if you wish to save the old settings. When you relaunch IGV, a new prefs.properties file is created with default settings.