Lift Genome Annotations

This tool converts genome coordinates and annotation files from the original to the new assembly using an alignment.  The input regions can be entered into the text box or uploaded as a file.  For files over 500Mb, use the command-line tool described in our LiftOver documentation.  If a pair of assemblies cannot be selected from the pull-down menus, a sequential lift may still be possible (e.g., mm9 to mm10 to mm39).  If your desired conversion is still not available, please contact us.

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

Minimum ratio of bases that must remap:  
Regions defined by chrom:start-end (BED 4 to BED 6)
Allow multiple output regions:  
  Minimum hit size in query:  
  Minimum chain size in target:  
Regions with an exon-intron structure (usually transcripts, BED 12)
Minimum ratio of alignment blocks or exons that must map:  
If exon 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. We do not recommend liftOver for SNPs that have rsIDs. See our FAQ for more information.

 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. See the LiftOver documentation.