For many analyses, one wants to measure the genome wide coverage of a feature file. For example, we often want to know what fraction of the genome is covered by 1 feature, 2 features, 3 features, etc. This is frequently crucial when assessing the "uniformity" of coverage from whole-genome sequencing. This is done with the versatile `genomecov` tool. How bedtools genomecov works As an example, let's produce a histogram of coverage of the exons throughout the genome. Like the `merge` tool, `genomecov` requires pre-sorted data. It also needs a genome file as above. Using the `-bg` option, one can also produce BEDGRAPH output which represents the "depth" fo feature coverage for each base pair in the genome: