Converts point coordinates between genome assemblies. Inspired by pyliftover, this offers a few advantages:
converter[chrom][pos]Install via pip: pip install liftover
from liftover import get_lifter
converter = get_lifter('hg19', 'hg38', one_based=True)
chrom = '1'
pos = 103786442
converter[chrom][pos]
# other synonyms for the lift call
converter.convert_coordinate(chrom, pos)
converter.query(chrom, pos)
# alternatively create a converter directly from a chainfile
from liftover import ChainFile
converter = ChainFile('/home/user/hg18ToHg38.over.chain.gz', one_based=True)
converter[chrom][pos]
# you can also specify an alternative website to load chain files from
converter = get_lifter('hg19', 'hg38', chain_server='https://www.example.com')
FAQs
Package for converting between genome build coordinates
We found that liftover demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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