From the documentation @http://info.gersteinlab.org/AlleleSeq:
Using the chain file, one can use the LifeOver tool to convert the annotation coordinates from reference genome to personal haplotypes.
However, when I tried to liftOver my bed file using maternal.chain, all returned unMapped.
10329 1 0
109 1 0
30199 3 0
My bed file:
chr1 14541 14542
chr1 14652 14653
chr1 14676 14677
chr1 14906 14907
It looked like the liftOver failed because of using different chromosome naming convention in .bed and .chain files. In .bed file chromosomes are named with prefix ‘chr’, while in chain files they don’t have such prefix.