From Genome Analysis Wiki
If the interest of qplot is a list of regions, e.g. exons, this can be achieved by providing a list of regions. The regions should be in the form of "chr start end label" each line in the file. In order for this option to work, within each chromosome (contig) the regions have to be sorted by starting position, and also the input bam files have to be sorted.
1 100 500 region_A
1 600 800 region_B
2 100 300 region_C
Qplot also provides the <code>--invertRegion</code> option. Enabling this option tells qplot to operate on those sequence bases that are outside the given region.