Use when computing genome-wide coverage from BED/GFF/VCF or BAM files, generating coverage histograms, BedGraph tracks, or per-position depth reports.
genomeCoverageBed -i features.bed -g genome.txt [options] or genomeCoverageBed -ibam reads.bam [options]/home/vimalinx/miniforge3/envs/bio/bin/genomeCoverageBedreferences/help.md-bg or -bga for browser visualization.-d or sparse zero-based depth with -dz.# 1) Default genome-wide histogram from BED intervals
genomeCoverageBed \
-i reads.bed \
-g genome.txt
# 2) BedGraph including zero-coverage intervals
genomeCoverageBed \
-ibam reads.sorted.bam \
-bga > coverage.bedgraph
# 3) Zero-based depth for non-zero positions only
genomeCoverageBed \
-ibam reads.sorted.bam \
-dz
default), BedGraph (-bg / -bga), or depth (-d / -dz).-split when spliced or blocked intervals should contribute as separate covered blocks.-scale, -strand, -pc, -5, or -3 only when the biological interpretation of coverage depends on those choices.-g is required unless you use -ibam.-bga includes zero-coverage intervals, whereas -bg omits them.-d is one-based and reports every genomic position; -dz is zero-based and reports only non-zero positions.-trackline is convenient for browser upload, but that first line must be removed before BedGraph-to-BigWig conversion.