bedtools OverlapBed computes the amount of overlap from two intervals

bedtools_overlapbed

Version	Tool Shed	Owner	Galaxy instances where the tool is available
2.30.0	toolshed.g2.bx.psu.edu	iuc	galaxy.genouest.org usegalaxy.be usegalaxy.eu usegalaxy.no
2.30.0	toolshed.g2.bx.psu.edu	iuc	usegalaxy.org usegalaxy.org.au
2.30.0	toolshed.g2.bx.psu.edu	iuc	usegalaxy.fr
2.29.2	toolshed.g2.bx.psu.edu	iuc	galaxy.genelab.nasa.gov galaxy.genouest.org treegenes.cam.uchc.edu usegalaxy.be usegalaxy.eu usegalaxy.fr usegalaxy.no usegalaxy.org.au
2.29.0	toolshed.g2.bx.psu.edu	iuc	galaxy.genouest.org usegalaxy.be usegalaxy.eu usegalaxy.fr usegalaxy.org usegalaxy.org.au
2.27.1	toolshed.g2.bx.psu.edu	iuc	bipaa-galaxy.genouest.org usegalaxy.be usegalaxy.org usegalaxy.org.au
2.27.1	toolshed.g2.bx.psu.edu	iuc	galaxy.mesocentre.uca.fr
2.27.1	toolshed.g2.bx.psu.edu	iuc	usegalaxy.eu
2.27.0.0	toolshed.g2.bx.psu.edu	iuc	bf2i-galaxy.insa-lyon.fr:8080 bipaa-galaxy.genouest.org usegalaxy.org
2.27.0.0	toolshed.g2.bx.psu.edu	iuc	galaxy.mesocentre.uca.fr
2.27.0.0	toolshed.g2.bx.psu.edu	iuc	usegalaxy.eu
2.27.0.0	toolshed.g2.bx.psu.edu	iuc	usegalaxy.org.au
2.27.0.0	toolshed.g2.bx.psu.edu	iuc	galaxy.sb-roscoff.fr usegalaxy.be
2.26.0.0	toolshed.g2.bx.psu.edu	iuc	bf2i-galaxy.insa-lyon.fr:8080
2.26.0.0	toolshed.g2.bx.psu.edu	iuc	bipaa-galaxy.genouest.org
2.26.0.0	toolshed.g2.bx.psu.edu	iuc	usegalaxy.eu usegalaxy.org
2.24.0	toolshed.g2.bx.psu.edu	iuc	usegalaxy.be usegalaxy.eu usegalaxy.org
2.22.0	toolshed.g2.bx.psu.edu	iuc	usegalaxy.eu
2.22.0	toolshed.g2.bx.psu.edu	iuc	usegalaxy.org
2.19.0	toolshed.g2.bx.psu.edu	iuc	usegalaxy.be usegalaxy.eu usegalaxy.no