IGV can use BEDTools to analyze data which is in view. BEDTools must be installed separately, and the account running IGV must have permission to execute the BEDTools files. 
BEDTools documentation is at http://code.google.com/p/bedtools/#Documentation
Of the many commands which BEDTools contains, IGV offers access to the following:

intersect

Identify regions of overlapping features in two tracks. Exons are treated as separate features (ie the "-split" flag is used)

subtract

Remove regions in one track from another. For example, if one had a track of features and wanted to find all regions NOT in a gene, one would subtract the gene track from the feature track

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closest

For each feature in the first track, find the closest matching feature in the second track. This may be an overlapping feature.

window

Similar to intersect, window searches for overlapping features. However, window adds a specified number (1000) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected

coverage

Calculate the coverage of track A by track B.
