LiftOver from GRCz11 to GRCz12tu

[Christian Pich]

I need to get new coordinates for variants for zebrafish (danio rerio). I have them for the assembly GRCz11 but need to obtain them for the latest assembly, GRCz12tu.

Do you have a way to do this?

thanks,

Christian

[Hiram Clawson]

Good Evening Christian:

You can use the liftOver files for such conversions:


https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/liftOver/danRer11ToGCF_049306965.1.over.chain.gz
and

https://hgdownload.soe.ucsc.edu/hubs/GCF/049/306/965/GCF_049306965.1/liftOver/GCF_049306965.1ToDanRer11.over.chain.gz

Note the discussion for this coordinate conversion procedure, in
the browser or using these files:

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert

--Hiram