Details of data cleaning have been reported previously (Nelson et al., 2012; Nelson et al., 2013). In brief, SNPs were excluded due to genotyping failure ( 23), call rate less than 95% (9), minor allele frequency less than 2% (47), and Hardy-Weinberg deviations (27). The mean call rate for SNPs remaining after data cleaning was 99.9%. All 1430 SNPs (shown in Supplementary Table 2) that remained after data cleaning were examined for association with PTSD. Data from samples were excluded due to phenotypic-genotypic gender mismatch, duplication due to participation in the project multiple times, and cryptic relatedness with identity by descent greater than 0.5.
