LiftOver is a necessary step to bring all genetical analysis to the same reference build. LiftOver can have three use cases:

1. Convert genome position from one genome assembly to another genome assembly.
In most scenarios, we have known genome positions in NCBI build 36 (UCSC hg 18) and hope to lift them over to NCBI build 37 (UCSC hg19).
2. Convert dbSNP rs number from one build to another.
3. Convert both genome position and dbSNP rs number over different versions.

The usage of liftOver in the terminal is as follows:

liftOver oldFile map.chain newFile unMapped

In this command, oldFile is the uploaded file in bed format. newFile is the file that successfully mapped and unMapped is the file that failed to be transformed. The map.chain file has the old genome as the target and the new genome as the query.

On this interface, you should select your source assembly and target assembly, and then upload the files to be converted. After submission, you will be able to download the result files after successful conversion and the failed files.

For a more flexible conversion, you may download the chain file from the DOWNLOAD section and run the liftOver on your local computer.

More detail about the liftOver, please visit LiftOver wiki.