Going through the process of trying to take imputation results from Build 37 to Build 38 (lifting up). I am aware of several tools out there that do this, like UCSC, NCBI, Crossmap, LiftoverPlink, etc., but I am having trouble getting an up-to-date chain file. We tried to use NCBI’s remap tool but the online version cannot handle files of any substantial size and the perl script will not work for us. The chain file that UCSC uses/provides is several years old (2013) so I was wondering if anyone has come across this problem and if you are aware of any more recent chain files that anyone may use? We would like to be able to use the liftover command line tool, but would like a newer chain file that is up-to-date, or atleast close to up-to-date with what NCBI currently has.
Why do you have concerns about the current chains? How many regions (%) are dropped if you use the current chains?
I have concerns about the older chain files, not the current. We ran liftover command line tool using the older chain files, took the snps that were not lifted over in this process, and ran them through ncbi's online remap tool. Using NCBI's remap tool, most of these snps did get lifted over, pushing us to believe that with a newer chain file, more snps will be lifted.