I'd like to run SAIGE and SAIGE-GENE for both autosomes and gonosomes (in sex-limited samples). I followed the SAIGE-doc, but the null model set up there excludes chrX and chrY, which throws an error if trying to run the association analyses for X or Y.
Is it valid to include chrX and chrY in the null model for this purpose?
If so, would it also be recommended to use that same model for the analysis of the autosomes for consistency?
Hey, this might be a very basic / naive question.
I'd like to run SAIGE and SAIGE-GENE for both autosomes and gonosomes (in sex-limited samples). I followed the SAIGE-doc, but the null model set up there excludes chrX and chrY, which throws an error if trying to run the association analyses for X or Y.
Is it valid to include chrX and chrY in the null model for this purpose? If so, would it also be recommended to use that same model for the analysis of the autosomes for consistency?
Any advice would be appreciated.