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A common task in bioinformatics is the mapping of DNA sequencing reads (produced by “next generation sequencing” experiments) against a reference genome. The output of the alignment is commonly encoded in a BAM file (Li et al., 2009). For several applications of DNA sequencing it is useful to extract the depth of coverage (Sims, Sudbery, Ilott, Heger, & Ponting, 2014) at specific positions in the BAM file, encoding the output in the standard BED format (Quinlan & Hall, 2010).

covtobed: a simple and fast tool to extract coverage tracks from BAM files