Samtools coverage computes the depth at each position or region

samtools_coverage

Version	Tool Shed	Owner	Galaxy instances where the tool is available
1.15.1+galaxy0	toolshed.g2.bx.psu.edu	iuc	usegalaxy.eu usegalaxy.fr
1.13	toolshed.g2.bx.psu.edu	iuc	galaxy.genouest.org usegalaxy.eu