X chromosome genotypes were processed separately from autosomal genotypes as additional care is required for pre-phasing, imputation, and post-imputation QC. At the genotype level, the pre-imputation QC steps for the X chromosome SNPs were the same as for the autosomes. An additional flag of -chrX was added when running SHAPEIT2 and IMPUTE2 software. Post-imputation, we employed the XWAS QC pipeline to remove variants in the pseudoautosomal regions (PARs), variants that were not in Hardy-Weinberg equilibrium in females, or variants with significantly different MAF (p<0.05/#SNPs) and differential missingness (P<10−7) between males and female controls (Gao et al. 2015).
