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
Usage notes: common usage involves specifying the genome file with -g, and the input alignments with -ibam
Applications: genomecov is used to estimate average sequencing depth, detect underrepresented regions, generate coverage tracks for