Is GEMMA able to run a bayesian sparse linear mixed model with the sex column?
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7.4 years ago
beausoleilmo ▴ 580

In a .fam file, I know that the column 1 to 6 are:

  1. Family ID ('FID')
  2. Within-family ID ('IID'; cannot be '0')
  3. Within-family ID of father ('0' if father isn't in dataset)
  4. Within-family ID of mother ('0' if mother isn't in dataset)
  5. Sex code ('1' = male, '2' = female, '0' = unknown)
  6. Phenotype value ('1' = control, '2' = case, '-9'/'0'/non-numeric = missing data if case/control)

I'm going to use GEMMA to run a BSLMM with this command:

gemma -bfile bird_noSca -bslmm 1 -w 5000000 -s 20000000 -n 1 2 3 4 5 6 -o bird_noSca_gemma1

I've looked in the manual and there is no place where they explain how to use the sex column. Is it possible to use it? how?

plink GWAS GEMMA fam • 1.7k views
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