Conversion of UCSC genome coordinates to those in NCBI

[Bob]

Hi,

 

Currently, NCBI and dbSNP only show genomic coordinates for GRCh38 and GRCh37.p13. There are substantial differences between GRCH37.p13 (and, of course, GRCh38) and the GRCh37 (Feb2009) build that you are using. Because two other utilities I am using (Affymetrix DMET and Ampliseq Designer for Ion PGM) are based on the GRCh37 (Feb2009) build and refer to your site, is there a convenient way to convert genomic coordinates for new SNPs in dbSNP to this older build? I would like to do this in batch format, as I have a large number of SNPs to convert.

 

Best regards,

Bob Rooney

Robert J. Rooney, PhD
Scientific Director/CSO
Genome Explorations Inc.
654 Jefferson Ave.
Memphis, TN 38105 USA
Tel: 901-405-4400
Fax: 901-578-5709
email: rro...@genome-explorations.com
web: www.genome-explorations.com


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[Steve Heitner]

Hello, Bob.

I just looked up a SNP ID at dbSNP and the coordinates appear to be in terms of GRCh38.  Patches to GRCh37 exist outside of GRCh37, so GRCh37 coordinates should be identical regardless of patch version.

That being said, we do have a liftOver utility to convert GRCh38 (hg38) coordinates to GRCh37 (hg19) coordinates at http://genome.ucsc.edu/cgi-bin/hgLiftOver.  The web utility is free for all to use.  We also have a downloadable standalone liftOver utility at http://hgdownload.cse.ucsc.edu/downloads.html#utilities_downloads.  This is free for academic, non-commercial and personal use, but would require the purchase of a license for commercial use.  Please see http://genome.ucsc.edu/license/ for further information.

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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