Software For Computing Residuals From Association Testing Of Snps Versus Expression Levels, Using A Linear Mixed Model

Question

[mdwain.uw]

Hi,

I'm looking for linear mixed model (LMM) software that will allow me to compute a residual, after correcting for fixed effects (i.e. covariates) and random effects due to genotype (i.e. using a relatedness matrix). Most software I have found (EMMA, EMMAX, etc.) do not output residuals. Does anyone know of such software?