IMPUTE2 reference allele: same as matrixEQTL?

Question

[User 7754]

When a dosage file is used for eQTL analysis using matrixEQTL, and the dosage file is with respect to a specific allele (e.g. the allele outputted as reference in IMPUTE2), is this also the reference allele used for the effect size computed in matrixEQTL?

Thanks!