igvtools provides a number of utilities to preprocess data files.

How to run a tool#

Select Tools > Run igvtools to open the igvtools window. This window allows you to select and run the tools: toTDF, Count, Sort, and Index.

  1. Select the tool that you want from the Command drop-down list.
  2. Specify the necessary files and/or genome.
  3. Select any of the alternative options you want.
  4. Click Run.

Information about the run will appear in the Messages box at the bottom of the window.

If you exit the IGV application, any tool that is in progress will be terminated.

You can also run the igvtools utilities from the command line, as described here.


The toTDF tool converts a sorted data input file to a binary tiled data (.tdf) file. Use this tool to pre-process large datasets for improved IGV performance. This tool was previously known as Tile.


Count computes average feature density over a specified window size across the genome. Common usages include computing coverage for alignment files and counting hits in Chip-seq experiments. By default, the resulting file will be displayed as a bar chart when loaded into IGV.


This command creates an index for an alignment file or a feature file. Index files are required for loading alignment files into IGV, and can significantly improve performance for large feature files. This command does not take an output file argument. Instead, the filename is generated by appending ".sai" (for alignments) or ".idx" (for features) to the input filename as IGV relies on this naming convention to find the index . The input file must be sorted by start position (see the Sort tool, below).

Note that you do not directly load the index file into IGV. Rather, IGV looks for a corresponding index file when the alignment or feature file is loaded.


Sort sorts the input file by start position.