liftOver

Reference Code backup Executable files

Convert genomic coordinates from one assembly (e.g. hg19) to another (e.g. hg38)

Category

Genomic Interval Manipulation

Usage

liftOver oldFile map.chain newFile unMapped

Manual

This tool is part of UCSC Genome Browser's utilities.
WARNING: liftOver was only designed to work between different assemblies of the same organism. It may not do what you want if you are lifting between different organisms. If there has been a rearrangement in one of the species, the size of the region being mapped may change dramatically after mapping.

Required arguments

  • oldFile: 
  • map.chain: 
  • newFile: 
  • unMapped:

oldFile and newFile are in bed format by default, but can be in GFF and maybe eventually others with the appropriate flags below. The map.chain file has the old genome as the target and the new genome as the query.

Options

  • -minMatch=0.N: Minimum ratio of bases that must remap. Default 0.95
  • -gff: File is in gff/gtf format. Note that the gff lines are converted separately. It would be good to have a separate check after this that the lines that make up a gene model still make a plausible gene after liftOver
  • -genePred: File is in genePred format
  • -sample: File is in sample format
  • -bedPlus=N: File is bed N+ format
  • -positions: File is in browser "position" format
  • -hasBin: File has bin value (used only with -bedPlus)
  • -tab: Separate by tabs rather than space (used only with -bedPlus)
  • -pslT: File is in psl format, map target side only
  • -ends=N: Lift the first and last N bases of each record and combine the result. This is useful for lifting large regions like BAC end pairs.
  • -minBlocks=0.N: Minimum ratio of alignment blocks or exons that must map (default 1.00)
  • -fudgeThick: (bed 12 or 12+ only) If thickStart/thickEnd is not mapped, use the closest mapped base. Recommended if using -minBlocks.
  • -multiple: Allow multiple output regions
  • -minChainT: Minimum chain size in target, when mapping to multiple output regions (default 0)
  • -minChainQ: Minimum chain size in query, when mapping to multiple output regions (default 0)
  • -minSizeT: deprecated, synonym for -minChainT (ENCODE compat.)
  • -minSizeQMin: matching region size in query with -multiple.
  • -chainTable: Used with -multiple, format is db.tablename, to extend chains from net (preserves dups)
  • -errorHelp: Explain error messages
     

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