[Genome] Obtaining allelle frequencies for rsid's

[nipun kakkar]

Hi All

I was looking for a table containing allele frequencies corresponding to
rsid's for dbsnp. Can anyone help?

[Pauline Fujita]

Hello,

We are currently preparing dbSNP 132 of the dbSNP track on the hg19
human assembly ready to release to our public site. Presently the data
are available on our test site (http://genome-test.cse.ucsc.edu/). You
are welcome to look at it on the test site with that caveat that the
data have not been through our quality assurance process yet.

Unfortunately we do not provide bulk downloads on the test site and the
table you are interested in "snp132" is a very large table. To access
this table using the table browser
(http://genome-test.cse.ucsc.edu/cgi-bin/hgTables) you will need to
limit your query to a list of rsIDs or a region of the genome (querying
the entire table will cause the site to time out). Specifically, in the
table browser once you have selected hg19 select:

group: Variation and Repeats
track: SNPs (132)
table: snp132
region: specify a region (and/or)
identifiers: you can paste a list of rsIDs
output: selected fields from primary and related tables

Clicking on submit then takes you to a menu where you can choose which
fields from the table to include in the output (i.e. "name" and
"alleleFreqs").

If you want a bulk download of the whole table and are satisfied with
the previous version of this track you can download the table from our
public site here:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

(see snp131.sql or snp131.txt.gz)


Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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[nipun kakkar]

What is the difference between snp131 which is available right now and
snp132 which will be available?. Can i grab the insertion deletion data from
the snp131 table with confidence for the hg19 genome build. ?

>
> Thanks,
> Nipun
>
>
>
>
>

[Brooke Rhead]

Hi Nipun,

Our snp131 table doesn't actually contain allele frequency data; we
changed our SNP table format to include allele frequencies starting with
snp132 (sorry if we didn't make that clear before).

To see the differences between the datasets, you can look at dbSNP's
summary page:

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi?view+summary=vi#buildStat

at the bottom of that page, there is a button to fetch a summary for the
previous build (131). Comparing those numbers shows that quite a few new
SNPs have been added in 132 (>30M in 132, <24M in 131).

I hope this helps you find the data you need. If you have further
questions, please feel free to contact us again at gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group