igvtools

The igvtools utility provides a set of tools for pre-processing data files. File names must contain an accepted file extension, e.g. test-xyz.bam. Tools include:

• toTDF
  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: .cn, .gct, .igv, .res, .snp, and .wig
  Note: This tool was previously known as tile

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

• index
  Creates an index file for an alignment or feature file.
  Index files are required for loading alignment files into IGV, and can significantly improve performance for large feature files. The file must be in sorted order by start position.
  Supported input file formats: .aligned, .bed, .psl, .sam, .bam, and .vcf (v3.2)

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

The igvtools can be run (1) directly from IGV,  or (2) downloaded as a separate utility and run from the command line.