Genotype calling for the 5.0 arrays was performed by Birdseed 26,27 and for the 500K arrays was performed by BRLMM. As basic QC filters for the data generated at the Broad Institute, we required that genotyping was >95% complete for each individual, and that each family had fewer than 10,000 Mendelian inheritance errors across the genome. We also required that each SNP had >95% genotyping, fewer than 15 Mendelian errors, Hardy-Weinberg Equilibrium P > 10−10, and minor allele frequency greater than 1%. For the AGRE sample, this left 2,883 high quality individuals genotyped for 399,147 SNPs with 99.6% average call rate. The basic filters for the data generated at Johns Hopkins were individual call rates > 95% for 5.0 arrays and > 90% for 500K arrays data, fewer than 5,000 Mendelian errors per family. Only monomorphic SNPs and those with greater than 50% missing data were dropped, for 498,216 SNPs. Our combined dataset had nearly 365,000 SNPs passing QC.
