Produce the coverage BED from a BAM file

bamtocov alignments.bam > coverage.bed

Use a target file to count the coverage in each region

bamtocov --regions target.bed --report target-stats.tsv alignments.bam > coverage.bed 

Generate a matrix from multiple outputs

The output of multiple files in BED format makes no sense, so at this moment we require to explicitly specifying a --skip-output flag. The report matrix is saved with --report (or -o).

bamtocov --regions target.bed --report target-stats.tsv --skip-output *.bam 

Count the coverage per target using legacy "covtobed" output

covtobed file.bam | covtotarget ...