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Old 03-25-2011, 12:22 PM   #1
JohnK
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Location: Los Angeles, China.

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Default dbSNP frequencies

I recently had someone ask for some dbSNP frequencies. Does anyone know what file to use to get MAF frequencies for SNPs with rsIDs listed by ID and, or allele? I've downloaded some files and can't seem to find the right one. I can't seem to use the 'contact' button on their web page either, because it continually tries to open up the wrong email client on my computer. Any help would be greatly appreciated. Thank you.

John
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Old 12-04-2013, 08:25 PM   #2
rajesh_mahato
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Hi,

You can download from UCSC table browser.


http://genome.ucsc.edu/cgi-bin/hgTab...a_outFileName=

just press on get output and you can select whatever field require for your research work.

Thanks
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Old 12-05-2013, 08:36 AM   #3
m_two
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VCF files for human and mouse can be retrieved here:

ftp://ftp.ncbi.nlm.nih.gov/snp/organ...uman_9606/VCF/
ftp://ftp.ncbi.nlm.nih.gov/snp/organ...use_10090/VCF/

Human files contain frequency information tagged as follows:
##INFO=<ID=GMAF,Number=1,Type=Float,Description="Global Minor Allele Frequency [0, 0.5]; global population is 1000GenomesProject phase 1 genotype data from 629 individuals, released in the 11-23-2010 dataset">

Frequency info can also be obtained from the NHLBI GO Exome Sequencing Project (ESP)
http://evs.gs.washington.edu/EVS/

Last edited by m_two; 12-05-2013 at 08:40 AM.
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