Genotyping was attempted with a total of 7681 samples, including 83 samples that were included as within-plate duplicates, 160 CEPH control samples, and 60 samples that were repeats of samples that had failed an initial genotyping attempt due to low call rate. The 7438 non-control samples (i.e., including those that failed the first attempt at genotyping and were re-genotyped) were subjected to five separate QC screens. These screens, along with the number (%) of samples failing each are: (1) non-calls in more than 5000 markers (N=130, 1.7%); (2) GenCall_50 score < .9009 (N=8, 0.1%); (3) GenCall_10 score < .75 (N=6, < 0.1%); (4) extreme heterozygosity or homozygosity (N=1, < 0.1%); () sample mixups or failure to confirm genetic relationship with other genotyped relatives (N=15, 0.2%). In total 160 (2.2%) of the non-control samples were eliminated, leaving a cleaned sample of 7278.
