Meta-analysis using Genome-Wide Association Meta-Analysis (GWAMA) tool
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Hi,

I am doing meta-analysis using GWAMA. However, I had a query. My data which I want to meta-analyze looks this

 SNP     CHR     POS      STR     IMP      EA       NEA      BETA     SE     P   r2-hat   r2-min
rs12562034  1  768448  +  minimac  A   G   4.9606e-02  4.8640e-01  3.0588e-01   0.9871  0.98237


All of the SNPs in my data is imputed using minimac, however the imputation score (r2-Hat) for some is high. The input file for GWAMA requires to have encoded for imputation using 0(not imputed) or 1(imputed) else it considers all SNPs to be genotyped.

My question is will it be ok to define a threshold, for example, those SNPs having r2 > 0.9 be considered as genotyped (0 in input file) and rest be imputed (1 in input file)? Or some other threshold would be useful? Is this a right way to encode for the SNPs?

I have tried to look for this papers but all I could find was that GWAMA is used, not the details of the imputation encoding.

Your help would be appreciated. Thanks.

SNP meta-analysis GWAS • 684 views