Hello,

I am using DS (imputed dosage) in vcf files for GWAS analysis (hl.logistic_regression_rows). I could generate gwas output using the function, .export( file_name ). And these are the header of my output file:

locus alleles AF rsid beta standard_error z_stat p_value fit

I’d like to add a couple of columns in the output file. The first one is imputation quality, R2, [observed dosage variance] / [expected dosage variance]. The second ones are sample sizes of cases and controls. Could you give some example code to compute some operations? Then, I might be able to compute the R2 and sample size.

Thanks,

Jaeyoon