Compute the coverage of a feature file among a genome.
genomeCoverageBed computes a histogram of feature coverage (e.g., aligned sequences) for a given genome. Optionally, by using the "Output type [depth]" option, it will report the depth of coverage at each base on each chromosome in the genome file.
Selecting "File A is BAM format [yes]" is analogous to using "-abam" option instead of "-a" in the command line version.
The output is a tab-delimited text file.
This tool uses the BEDTools package. Please cite the article:
Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.
Please see the BEDTools homepage for more details.