Move annotations from one assembly to another

liftOver oldFile map.chain newFile unMapped
oldFile and newFile are in bed format by default, but can be in GFF and
maybe eventually others with the appropriate flags below.
The map.chain file has the old genome as the target and the new genome
as the query.

WARNING: liftOver was only designed to work between different
assemblies of the same organism. It may

This is a companion discussion topic for the original entry at quay.io/cancercollaboratory/dockstore-tool-liftover