pybedtools.bedtool.BedTool.liftover

BedTool.liftover(chainfile: str, unmapped: str | None = None, liftover_args: str = '') → BedTool

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.