Lift Genome Annotations

This tool converts genome coordinates and genome annotation files between assemblies.  The input data can be pasted into the text box or uploaded from a file.  For more information, please see our LiftOver documentation.  If a pair of assemblies cannot be selected from the pull-down menus, a sequential lift may still be possible.  For example, to lift from mm9 to mm39, lift from Mouse mm9 to mm10 and then from mm10 to mm39.  

Original Genome: Original Assembly: New Genome: New Assembly:


Minimum ratio of bases that must remap:
BED 4 to BED 6 Options
Allow multiple output regions:
  Minimum hit size in query:
  Minimum chain size in target:
BED 12 Options
Min ratio of alignment blocks or exons that must map:
If thickStart/thickEnd is not mapped, use the closest mapped base:

 Paste in data below, one position per line. You can use the BED format (e.g. "chr4 100000 100001", 0-based) or the format of the position box ("chr4:100,001-100,001", 1-based). See the documentation.

 Or upload data from a file (BED or chrN:start-end in plain text format):

Command Line Tool

To lift genome annotations locally on Linux systems, download the liftOver executable and the appropriate chain file. Run liftOver with no arguments to see the usage message.