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Old 06-26-2013, 02:22 PM   #1
MikeDacre
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Location: Stanford

Join Date: Jul 2011
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Question Plink for meta-analysis of quantitative traits

Hi All,

I am attempting to do a meta-analysis of a quantitative trait using plink and METAL. I am running plink with the '--assoc' (and no other modifications) to get a .qassoc file. The problem is that this file does not include the allele names or the frequency of the major and minor alleles in the population.

I can't seem to find a way to add this in, other than calculating it manually and adding it after. Is there a way to include this information to run with METAL/GWAToolbox, or even with plink's meta-analysis (right now I have to specify 'no-allele').

Thanks,

Mike
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