We performed QC on each genotyping batch separately with the following steps: (1) SNPs with genotype missing rate >0.05 were removed; (2) samples with genotype missing rate >0.02 or absolute value of heterozygosity >0.2, or samples that failed sex checks were excluded; (3) SNPs with missing rate >0.02, or HWE test P < 1 × 10−6 were discarded. We then removed SNPs that showed significant batch associations with P < 1 × 10−6, and merged genotyping batches for subsequent processing and analyses.
