hg19tob37 chain file

[Pranav Singh]

Hello I am downloading WXS data from TCGA and I am attempting to convert UCSC hg19 annotation coordinates to the hg19_Broad or b37 reference genome. Is there a hg19 to b37 chain file that you can provide.

Sincerely,

Pranav Singh

University of California, San Diego

[Steve Heitner]

Hello, Pranav.

We do not have such a liftOver file, but there are other resources available to you.  I looked on Biostars and others have also experienced the same issue.  You will be interested in the post at https://www.biostars.org/p/101543/.  A web search of “hg19 to b37” will turn up similar results.  You also always have the option to create your own liftOver files.  You may be interested in the previously-answered question at https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/b_wmmAvdNZw/Bh7BVs2MEiYJ.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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