I've been seeing mixed responses or unclear responses to this question on the forums so I was wondering if anyone might be able to clarify the matter. My understanding is that the liftover utility is generally a good tool for mapping between builds, yet I've seen it mentioned on the forums that mapping dbSNP 132 from hg19 to hg18 coordinates as well as the latest 1000 genomes release for hg19 to hg18 is not so trivial. Can anyone comment on their experience with using liftover to map variant annotations from hg19 to hg18 coordinate space? How accurate is it? For those regions producing innacurate results...does anyone have any advice to overcome the difficulty?
Just found this: ftp://ftp.ensembl.org/pub/misc-scripts/Assembly_mapper_1.0/
Anyone had any success with it? I'm going to be trying it out. Will post my experience with it