Hi, this may be a very obvious question, but I'm new to this and can't find any answers online.
I have a dataset that was converted to the UCSC bed format for LiftOver, and now I need to use this updated dataset for pre-phasing and imputation. Is there an easy way to take the LiftOver output and change it into something that SHAPEIT and/or IMPUTE2 can use?
The best option I can see is changing the bed file to a PLINK map file, but that would involve a lot of text editing and merging of files. Any advice would be greatly appreciated.