genomecov

genomecov is a command in the BEDTools software suite that computes sequencing coverage across a reference genome from alignment data. It can summarize coverage at the base level or as contiguous blocks, and is commonly used to assess sequencing depth, identify regions of low or zero coverage, and support downstream normalization and visualization tasks. The tool is applicable to diverse data types, including whole-genome and RNA-seq experiments.

Input and output: genomecov typically operates on a BAM or CRAM file containing read alignments, together with a genome file that provides chromosome sizes. Output formats vary by option: per-base coverage can be written as a simple table, while options such as -bg produce bedGraph-like blocks for regions with nonzero depth, and -dz outputs a per-base depth record. The -split option allows splitting alignments at spliced junctions, which is especially important for RNA-seq data. A -max option can cap depth values to a specified threshold, aiding visualization and downstream processing.

Usage notes: common usage involves specifying the genome file with -g, and the input alignments with -ibam (or other supported input forms). The choice of output mode (-bg, -dz, or default) determines how the coverage information is presented, influencing ease of integration with genome browsers or downstream analyses. The tool is part of the BEDTools suite and is frequently used in conjunction with other BEDTools utilities for more complex coverage analyses.

Applications: genomecov is used to estimate average sequencing depth, detect underrepresented regions, generate coverage tracks for genome browsers, and perform quality control on sequencing experiments. It provides a straightforward, strand-aware or strand-specific, and spliced-aware approach to summarizing coverage across a genome.