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)
Keep original positions in output:  
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 your data below, using one position per line. Supported formats include BED (e.g. "chr4 100000 100001", 0-based) and position box ("chr4:100,001-100,001", 1-based). Refer to the documentation for detailed information. LiftOver is not recommended for SNPs with rsIDs; refer to our FAQ for additional information. For information on errors in the LiftOver output, see our FAQ.

 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.