Covarites in GWAS via GCTA

Question

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Hi all,

I'm trying to do gwas (fastGWA-GLMM) with ~ 20K samples and would like to include a contemporary group as a categorical covariate. The covariate file format is FID IID CG. I'm using fastGWA-GLMM as in the command below

gcta-1.94.1 --mbfile geno_chr.txt --grm-sparse UKB_SAS_phen_updated_sparse --fastGWA-mlm-binary  --joint-covar --pheno UKB_SAS.phen --covar batch.txt  --out UKB_SAS_phen_updated_fastgwa_sp_GRM --thread-num 6  

However, when running the command, I get the error "Error: too many levels in covariate #1. You may fit it as a quantitative covariate using --qcovar." The software says I need to use this covariate as a quantitative covariate but it is not true. How can I solve it?

Cheers,

Answer 1

[GCL]

Hi,

I got the same problem when running a GWA using fastGWA. If possible, an option to go around this problem is to break down the contemporary groups into multiple covariates. Although it does not fix the problem, it may be good enough for the analysis. For example, let's say your contemporary group is a combination of levels of X, Y, and Z, such as XYZ. Then, you can break it into three covariates X, Y, and Z, each with lower levels than in your contemporary group.

Please, let me know if you figured out how to solve the "Error: too many levels in covariate #1. You may fit it as a quantitative covariate using --qcovar.".

Cheers,