LiftUp format

LiftUp can convert coordinates in most annotation files. It can add to positions and change the chromosome part of those files. It's main input is the lift-file that specifies how to convert the coordinates.

The format is:

offset oldName oldSize newName newSize

An example:

 0       frag1   1000    chr1    5000
 1001    frag2   1000    chr1    1000

Typing this command:

 liftUp stdout -type=.bed test.lft warn test.bed

will lift the following feature

 frag2   1100    1200    voila

to the following one:

 chr1    2101    2201    voila