IGV : tracks for normalize coverage Data (need igvtools to make .tdf files)

https://software.broadinstitute.org/software/igv/igvtools
https://software.broadinstitute.org/software/igv/igvtools_commandline

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 ASCII 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 

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

igvtools count

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

Usage:
          igvtools count [options] [inputFile] [outputFile] [genome]

 The input file must be sorted by start position

http://software.broadinstitute.org/software/igv/book/export/html/6

To load normalized coverage track to IGV

View -> Preferences -> Tracks

Select to normalize tracks containing coverage data in .tdf files that were created using igvtools.  This normalization option multiplies each value by [1,000,000 / (totalReadCount)].

• This is only available for .tdf files created using igvtools builds dated 1/28/2010 or later.  Earlier versions of igvtools did not record the total read count.
• This selection takes effect with new sessions loaded afterwards.