When specifying this, rvtests can output genotypes, phenotype, covariates (if any) and collapsed genotype to tabular files
However, when I use this option, I only see the raw genotype dosages for each SNP in the output file. What is the collapsed genotype supposed to be? Is there a way to output the raw burden level for each individual/gene, i.e. counts of rare variants, for input into another program in R?
Under documentation for utility models, I see:
However, when I use this option, I only see the raw genotype dosages for each SNP in the output file. What is the collapsed genotype supposed to be? Is there a way to output the raw burden level for each individual/gene, i.e. counts of rare variants, for input into another program in R?