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.
java -jar picard.jar LiftOverIntervalList I=input.interval_list O=output.interval_list SD=reference_sequence.dict CHAIN=build.chain
INPUT (File) Interval list to be lifted over. Required.
OUTPUT (File) Where to write lifted-over interval list. Required.
SEQUENCE_DICTIONARY (File) Sequence dictionary to write into the output interval list. Required.
CHAIN (File) Chain file that guides LiftOver. Required.
MIN_LIFTOVER_PCT (Double) Minimum percentage of bases in each input interval that must map to output interval. Default value: 0.95. This option can be set to 'null' to clear the default value.