Measure genome-wide coverage

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.

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: