[BioC] where to get chr_rpts file for dbSNP human 36.3 assembly

Hervé Pagès hpages at fhcrc.org
Tue Nov 1 23:34:39 CET 2011

Hi Shirley,

On 11-11-01 01:51 PM, shirley zhang wrote:
> Dear list,
> In terms of dbSNP database in NCBI, I can get the chr_rpts files for
> the most recent 37.3 assembly from the following FTP site,
> ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/chr_rpts/
> My question is how/where I can get these chr_rpts files based on the
> 36.3 assembly

Please don't cross post. This sounds like a question for the dbSNP

FWIW, right now it doesn't seem like those files have been updated yet:
they are still from August 15 (i.e. dbSNP build 134, based on reference
genome GRCh37.p2). AFAIK the last build based of the 36.3 assembly was
dbSNP build 130.

Not sure what you want to do with those files, but if you only need
to access the genome coordinates and alleles of your SNPs, you might
want to have a look at the SNPlocs.* packages.

Alternatively, you could always use a tool like UCSC liftOver (also
available in Bioconductor, in the rtracklayer package) to remap things
between different genome assemblies.


> Thanks,
> Shirley
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Hervé Pagès

Program in Computational Biology
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