Running IGV with a batch file
As of version 1.5, a user can load a text file to execute a series of sequential tasks by using Tools>Run Batch Script. The user loads a TXT file that contains a list of commands, one per line, that will be run by IGV. Arguments are delimited by spaces (NOTE: not tabs). Lines beginning with # or // are are skipped. See Controlling IGV through a Port for accepted commands.
The example script does the following: