3725. Imputation was done for a window of 5 Mb at a time with IMPUTE226 using phased reference panel from 1000 Genome Project phase 3 data set. The imputed data were reassembled with GTOOL. The following criteria were used for QC filtering with PLINK: minimum threshold for a minor allele frequency of 0.01, maximum individual missingness rate of 0.1, and Hardy–Weinberg equilibrium p-value of 0.001. A total of 9,831,409 variants survived this QC filtering step. Of note, our target SysBio cohort participants were completely independent of the discovery GWAS cohort of the PGC-PTSD study.
