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?