igvtools

The igvtools utility provides a set of tools for pre-processing data files.  These include:

• tile
  Converts a sorted data input file to a binary tiled data (.tdf) file. 
  Used to preprocess large datasets for improved IGV performance.
  Supported input file formats: .wig, .cn, .snp, .igv, .res, and .gct

• count
  Computes average alignment or feature density for over a specified window size across the genome. 
  Used to create a track that can be displayed in IGV, for example as a bar chart.
  Supported input file formats: .sam, .bam, .aligned, .psl, .pslx, and .bed

• index
  Creates an index file for an ASCII alignment or feature file.
  Index files are required for loading alignment files into IGV, and can significantly improve performance for large feature files.
  Supported input file formats: .sam, .aligned, .vcf, .psl, and .bed

• sort
  Sorts the input file by start position. 
  Used to prepare data files for tools that required sorted input files.
  Supported input file formats: .cn, .igv, .sam, .aligned, .psl, .bed, and .vcf

From IGV: igvtools is accessed by selecting Tools>Run igvtools...

Command line: The igvtools commands can also be run from the command line.  To install, download the igvtools zip file from the Downloads page.  On Windows, enter the commands at an MS-DOS prompt (select Start>Run and type: cmd). On Mac, enter the commands in a terminal window (select Applications>Utilities>Terminal).