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On sites like SNPedia, some pages contain the frequency of the SNP in question in different populations, based on published research. I'm trying to write a script that takes 23andme data and compares it with SNP frequency to find rare SNPs that the user possesses. I'm thinking that the only way to do this might be to scrape it from a SNP database. Is there anywhere you know of that makes this information available in a more accessible format, ideally preformatted for parsing?

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  • $\begingroup$ I found what would be a good source, but the links are dead: snp.cshl.org/downloads/index.html.en $\endgroup$ – Mike May 22 '13 at 19:48
  • $\begingroup$ Here's another, but it's about as clear as mud: useast.ensembl.org/info/docs/api/variation/… $\endgroup$ – Mike May 22 '13 at 19:52
  • $\begingroup$ There was also the Frequency Finder, but the NIH mirror and so is the UChicago mirror (which Google suggests was hacked): bioinformatics.oxfordjournals.org/content/20/3/439.full.pdf $\endgroup$ – Mike May 22 '13 at 19:59
  • $\begingroup$ I encountered the same problem about a year ago. After digging through several databases, the only answer I could come up with was the 1000 genomes project. That's when I let the dream die, but would certainly be interested if you decided to tackle it. $\endgroup$ – Alexander D. Scouras May 23 '13 at 8:26
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You might be able to get some raw data on SNP frequency by batch querying the dbSNP database. I have not used it myself, though.

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This is one of the reasons the 1000 genomes project was created.

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Have you looked at ALFRED (The ALlele FREquency Database)? The data is from 2011, but seems extensive and has downloadable zip files at http://alfred.med.yale.edu/alfred/alfredDataDownload.asp

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