BedTool.liftover(chainfile, unmapped=None, liftover_args='')[source]

Returns a new BedTool of the liftedOver features, saving the unmapped ones as unmapped. If unmapped is None, then discards the unmapped features.

liftover_args is a string of additional args that is passed, verbatim, to liftOver.

Needs liftOver from UCSC to be on the path and a chainfile downloaded from UCSC.