What it does

The IGVTools count command 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.

To cite your use of IGV in your publication:

James T. Robinson, Helga Thorvaldsdottir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov.
Integrative Genomics Viewer.  Nature Biotechnology 29, 24-26 (2011)

Input formats

Supported input file formats are: .sam, .bam, .aligned, .psl, .pslx, and .bed.

Outputs

The output formats are IGV tiled data file (TDF) file (.tdf) and/or WIG file (.wig)

IGVTools count parameter list

This is an exhaustive list of igvtools count options:

For count:

-z Integer        Specifies the maximum zoom level to precompute. The default
                  value is 7 and is sufficient for most files. To reduce file
                  size at the expense of IGV performance this value can be
                  reduced.

-w Integer        The window size over which coverage is averaged. Defaults to 25 bp.

-e Integer        The read or feature is extended by the specified distance
                  in bp prior to counting. This option is useful for chip-seq
                  and rna-seq applications. The value is generally set to the
                  average fragment length of the library.

-f list           A comma delimited list specifying window functions to use
                  when reducing the data to precomputed tiles.   Possible
                  values are  min, max, and mean.  By default only the mean
                  is calculated.