LiftOver from GRCz11 to GRCz12tu

Christian Pich

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Jun 13, 2026, 1:30:24 AMJun 13

to UCSC Genome Browser Public Support

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

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Jun 13, 2026, 3:38:58 AMJun 13

to Christian Pich, UCSC Genome Browser Public Support

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

Christian Pich

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Jun 15, 2026, 5:00:33 AMJun 15

to UCSC Genome Browser Public Support, Hiram Clawson, UCSC Genome Browser Public Support, Christian Pich

Hallo Hiram,

thank you for the info and links. That is very helpful.

Christian

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