GxE interaction

[DelnazRoshandel]

I want to run a GWAS for a quantitative trait in UKBB on RAP and test for GxSex interaction. So in step 1, I included Sex as a covariate in the model with a bunch of other covariates. I realize that --interaction can only be used in Step 2. So My code looks like this:

regenie --step 1 \ --lowmem --out Output_File_Name --bed ukb22418_c1_22_v2_merged \ --phenoFile Phenotype_File.txt --covarFile Covariates_File.txt \ --phenoCol PhenotypeName \ --covarColList Sex,Covar1,Covar2,... \ --catCovarList Sex \ --bsize 1000 --threads 16

Which worked fine. However, when I run Step 2 like this:

regenie --step 2 \ --bgen ukb22828_c1_b0_v3.bgen \ --sample ukb22828_c1_b0_v3.sample \ --phenoFile Phenotype_File.txt --covarFile Covariates_File.txt \ --phenoCol PhenotypeName \ --covarColList Sex,Covar1,Covar2,... \ --catCovarList Sex \ --interaction Sex \ --minMAC 80 --minINFO 0.5 \ --bsize 1000 \ --pred Output_File_Name.list \ --threads 16 --out Output_File_Name_Chr1

I get this error message: ERROR: There are unmatched arguments: '--covarColList' (Make sure there are no spaces in the options arguments)

There is no space between the covariate names. They are separated by ","

I am wondering what is causing the problem.

[joellembatchou]

Hi,

Have you trying printing your command and piping through cat -A to see if there are any special characters?

Cheers, Joelle

[DelnazRoshandel]

Thanks Joelle. I realized where the problem comes from. On Rap when I start the line with tab instead of space even though I put space before \ at the end of the line before, it puts no space between the commands in the two lines. So one needs to make sure to start each line with space.