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Starting with a a few human single nucleotide polymorphisms (SNPs) how can I query a database of all known SNPS such that I can generate a list (data.table or csv file) of the 1000 or so closest SNPS, weather or not the SNP is a tagSNP, and what the minor allele frequency (MAF) is and how many bases it is away from the starting SNPS?

I would prefer to do this in R (although it does not have to be). Which database should I use? My only starting point would be listing the the starting snps (eg rs3091244 , rs6311, etc).

I am certain there is a nice simple Bioconductor package that could be my starting point. But what? Have you ever done it? I imagine it can be done in about 3 to 5 lines of code.

seaotternerd
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Farrel
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    As this isn't really a programming question, it doesn't belong on this site. – nograpes Oct 09 '13 at 13:31
  • @nograpes I tried searching Stackexchange to see what would be the best site and it was either here or biology. It is the interface of the two. Too data/databasey for biology and too simple for programming. – Farrel Oct 09 '13 at 13:34
  • It really isn't the interface of the two, it is mostly about finding a database, which doesn't belong on this site. If you can't post some data, code, and a problem, it probably doesn't belong on Stack Overflow. – nograpes Oct 09 '13 at 13:38
  • How about "Open Data.SXC"? – Eekhoorn Oct 09 '13 at 15:32
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    On http://opendata.stackexchange.com/q/1180/422 someone reminded me of the absolutely obvious place that this should have been posted: http://www.biostars.org/. I had forgotten about biostars because it is no longer part of stackexchange. Sorry! – Farrel Oct 09 '13 at 22:32
  • @Farrel it would be nice if you could add the link to the post at biostars.org. – zx8754 May 25 '16 at 13:13

1 Answers1

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Again this is off topic but you can actually do all of the things you mention through this web based tool from the BROAD:

http://www.broadinstitute.org/mpg/snap/ldsearch.php

You just input a snp and it gives you the surrounding window of snps, and you can export to csv as well.

Good luck with your genetics project!

qwwqwwq
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