Use liftOver provided from UCSC web site.
The liftOver is designed to work between differenct assemblies of the same organism. This program does not have multiple alignment function but allows to lift genomic coordinates in the same organism. So, this requires a map.chain file which has the old genome as the target and the new genome as the query. For human genome you can get it at UCSC download page.
Usage: liftOver oldFile map.chain newFile unMapped
oldFile : BED format (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) (optional)
==> It works with a input file having first 3 columns only. All positions MUST be zero base.
newFile : output file name
unMapped: output file name for un-lifted positions
ex) ./liftOver hg18.positions hg18ToHg19.over.chain ./output/hg19.positions ./output/unmapped.positions
Download liftOver: (http://hgdownload.cse.ucsc.edu/admin/exe/)