Lift over variants, positions, or intervals from one reference genome to another.
This web interface supports more input formats and requires fewer clicks than existing interfaces like
UCSC LiftOver and
Ensembl Assembly Converter.
Under the hood, it uses the
UCSC liftOver command-line tool for
intervals and
positions,
while for
variants it uses a new
bcftools plugin which avoids many of the
limitations of other liftover tools (particularly for indels) as described in [
Genovese 2024]. All chain files were downloaded from UCSC.
We use the
GeneBe API to convert HGVS notation to genomic coordinates for hg38, and to provide variant consequences for both hg19 and hg38. The
Ensembl API is still used to convert HGVS notation for hg19, and as a fallback when GeneBe cannot convert an HGVS variant.
To submit issues or feature requests, please use
broadinstitute/liftover/issues.