I am trying to translate (lift over) bed files describing genomic regions from hg37 to hg38. I have tried both UCSC's LiftOver tool and CrossMap but saw that they give me different results. I therefore need a way of assessing how correct the results are.
I decided to test by downloading a bed file of the RefSeq genes for hg37 and one for hg38 from UCSC. Then, I run
liftOver to translate the hg37 file to hg39 coordinates and now I want to compare the results of the liftover to the bed file I downloaded for hg38.
How can I usefully compare these files? I am hoping for a tool that can report how similar the two are. Ideally, I would like to see three things in the output:
- Matching regions: those that are shown with identical positions in the liftover results and the UCSC bed file.
- Non-matching regions: those whose coordinates do not match between the two files.
- (if possible) fuzzy matches: those that are not identical but pretty close (off by a few nucleotides).
I thought it would be easy to do with a little awk script but it gets quite complicated because certain RefSeq genes are mapped to multiple positions (e.g. MIR4454). And the 3rd requirement (fuzzy) is not trivial to do in awk. I can live without that though, if a tool can give me the other two.