LiftOver
Description
This tool converts genome coordinates and genome annotation files between assemblies.
License
Freely available for academic, nonprofit, and personal use (https://genome.ucsc.edu/license/gblicense.pdf)
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of liftover and load default version of liftover as
module avail liftover/ # list available modules module load liftover # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail liftover
and choose explicit version you want to use.
Documentation
https://genome.ucsc.edu/cgi-bin/hgLiftOver