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 $\endgroup$– MikeCommented May 22, 2013 at 19:48
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$\begingroup$ Here's another, but it's about as clear as mud: useast.ensembl.org/info/docs/api/variation/… $\endgroup$– MikeCommented May 22, 2013 at 19:52
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$\begingroup$ 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 $\endgroup$– MikeCommented May 22, 2013 at 19:59
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$\begingroup$ 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. ScourasCommented May 23, 2013 at 8:26
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3 Answers
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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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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
