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

Birolo, Giovanni; Telatin, Andrea

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. For several applications of DNA sequencing it is useful to extract the depth of coverage at specific positions in the BAM file, encoding the output in the standard BED format.

Here we describe covtobed, a C++ program designed to extract the depth of coverage per position from a sorted BAM file, optionally specifying a range of coverage of interest and a minimum length for the features to be printed in the output BED file. Parsing of BAM files is performed using libbamtools.

The design has been inspired by the UNIX programming philosophy, and thus covtobed performs a single task and supports input and output streams.

This is a copy of the repository, release v1.1.0: https://github.com/telatin/covtobed/

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