Description

Lifts over an interval list from one reference build to another. This tool adjusts the coordinates in an interval list derived from one reference to match a new reference, based on a chain file that describes the correspondence between the two references. It is based on the UCSC liftOver tool (see: http://genome.ucsc.edu/cgi-bin/hgLiftOver) and uses a UCSC chain file to guide its operation. It accepts both Picard interval_list files or VCF files as interval inputs.