Introduction

In bioinformatics, a common task is to align several (usually short) DNA sequences against a reference sequence (e. g. a complete genome of the organism).

_{The screenshot of shows the alignment of several short DNA sequences (reads) against a reference genome. The program graphically displays the coverage track}

IGV itself displays a coverage track, but for computational reasons only if the zoom is below 50 kbp. On the other hand, it is possible to visualize a BED track spanning the whole chromosome.

covtobed reads an alignment file in BAM format and prints a BED track with the nucleotide coverage and can be used to select the regions with a coverage of interest (e. g. uncovered regions with 0X coverage, low coverage regions <5X, etc.).

For a more detailed introduction to coverage analysis see: Coverage Analysis from the Command Line.