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. If a pair of assemblies cannot be selected from the pull-down menus, a direct lift between them is unavailable.

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 (BED or chrN:start-end formats):

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.