I started with PLINK data files, and changed the .map file over to the UCSC .bed format in order to do LiftOver. Now I have the output from that (in UCSC .bed format), and need to get it ready for Impute2, but cannot figure how to change it into Impute2's required input format.
At this point, I'd even take advice on how to get my UCSC .bed files back into PLINK format, as it seems like I could alternatively feed it into SHAPEIT and then into IMPUTE2.
I'm completely stuck and any help is greatly appreciated!!