Matching genomic regions / Genome coverage BED

Description

Compute the coverage of a feature file among a genome.

Parameters

• Input file is BAM format (yes, no) [no]
• Output type (histogram, depth, BedGraph, BedGraph-all) [histogram]
• Treat split BAM or BED12 entries as distinct BED intervals (yes, no) [no]
• Calculate coverage from specific strand (both, +, -) [both]
• Combine positions by depth (yes, no) [no]
• Max depth (Integer) [1]

Details

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.

Output

The output is a tab-delimited text file.

References

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.