Plink for meta-analysis of quantitative traits

[MikeDacre]

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