Post by pierre on Jul 5, 2023 3:43:27 GMT
Hi,
I'm trying to do gwas on UK biobank subset ~ 8,200 samples and would like to include batch number (95 batches) as covariate. The covariate file format is FID IID b[batch#] 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'm getting this error "Error: too many levels in covariate #1. You may fit it as a quantitative covariate using --qcovar."
Is there a work around for this?
Cheers,
Pierre
I'm trying to do gwas on UK biobank subset ~ 8,200 samples and would like to include batch number (95 batches) as covariate. The covariate file format is FID IID b[batch#] 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'm getting this error "Error: too many levels in covariate #1. You may fit it as a quantitative covariate using --qcovar."
Is there a work around for this?
Cheers,
Pierre