For imputation, we included those samples that passed both autosomal QC, and had a call rate >0.98 on the X chromosome. Furthermore, because we could not use the same case/pseudo-control design for the trio data (i.e. due to lack of a non-transmitted X chromosome from the fathers of affected females), we included only the affected individuals from the trio data, ancestry-matched them to controls from the case/control dataset, and analyzed them with the case/control data. We performed PCA using EIGENSOFT and removed any trio cases without matched controls.
