Lifts over a VCF file from one reference build to another. This tool adjusts the coordinates of variants within a VCF file to match a new reference. The output file will be sorted and indexed using the target reference build. To be clear, REFERENCE_SEQUENCE should be the target reference build. The tool 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. Note that records may be rejected because they cannot be lifted over or because of sequence incompatibilities between the source and target reference genomes. Rejected records will be emitted with filters to the REJECT file, using the source genome coordinates.
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