It did go through.  I am not too familiar with these packages.  You might
check the 1000 genomes calls to get a third vote, as at least some of the
samples
should be present in the 1000 genomes VCF.


On Tue, Apr 15, 2014 at 8:11 AM, Naomi Altman <naomi@stat.psu.edu> wrote:

> This did not seem to go through the first time. --Naomi
>
>
> -------- Original Message --------
> Subject:        GWASdata
> Date:   Mon, 14 Apr 2014 14:15:54 -0400
> From:   Naomi Altman <naomi@stat.psu.edu>
> To:     Bioconductor mailing list <bioconductor@r-project.org>
>
>
>
> I have been trying out some of the SNP tools using the GWASdata data
> sets.  One thing I did was to look for differences in genotype calls
> between the Affy and Illumina data for what appear to be the same
> subjects (they have the same subject and family id).  They are highly
> discrepant.  At first I thought that the A and B alleles were switched,
> but swopping the 0's and 2's did not change the magnitude of number of
> discrepancies.  The SNPs appear to be in the same order.
>
> Have I misinterpreted something?
>
> --Naomi
>
>
>
>
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