I am interested in using Hail to lift over my VCFs from GRCh37 to 38. However, I could not find in the documentation whether the variant alleles are converted in the liftover process, whether strand flips are annotated, and whether the indels are left normalized. Could someone point me to the relevant code/documentation? Thanks!
Apologies for reverting to you a bit late! The documentation for liftover can be found here: https://hail.is/docs/0.2/guides/genetics.html#liftover-howto