Re: [Gmod-help] GWAS

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Re: [Gmod-help] GWAS

Scott Cain
Hi Ben,

I hope you and your family are well.  I'm cc'ing this to the schema
mailing list to get it a wider audience.

Actually, Chado does do genotypes and phenotypes, but I don't recall
anyone off hand putting GWAS data into Chado.  I imagine it could be
done, and having a loader for it would be really nice.  It might even
be possible to write a (relatively) simple loader with
Bio::Chado::Schema, a DBIx::Class-based interface for the Chado
schema.

Anyone else got a loader for GWAS data?

Scott


On Thu, Jul 22, 2010 at 3:49 PM, bfaga <[hidden email]> wrote:

> Hey everyone,
>
> Is there GMOD utility that would suck in genotype data from a GWAS study,
> maybe store it in a Chado db and export the files that are used for linkage
> and association analysis software such as plink and merlin?
>
> A cursory search came up with nothing (and I recall that chado doesn't do
> genotype data) but I thought it was worth a shot to ask.
>
> Ben



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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