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,