Does liftover update alleles

[hyslin]

When I applied liftover from GRCh38 to GRCh37 on my Hail table, the process was pretty fast but it didn’t seem to update the alleles. Does liftover also change the alleles? If not, what is the recommended way to update them?

rg37 = hl.get_reference(‘GRCh37’)
rg38 = hl.get_reference(‘GRCh38’)
rg38.add_liftover(‘gs://hail-common/references/grch38_to_grch37.over.chain.gz’, rg37)

qc_var_hg19 = qc_var.annotate(locus_grch37 = hl.liftover(qc_var.locus, ‘GRCh37’))

[chrisvittal]

It does not, it only updates loci. There is no official recommended way to update them. You can check to see if the allele has changed strand using hl.liftover(..., include_strand=True).

Our guide on how to use the liftover function is linked below:

Hail | Genetics