BAM file matched to the expected individual in the SNP genotype data, the sample was accepted if its chipmix and freemix parameters were both below 0.2 (Fig. 7). Higher values for chipmix and freemix can indicate contamination, so samples exceeding this cutoff were excluded. Alternatively, If a BAM file did not match to the expected individual in the SNP genotype data, the sample was excluded except in 4 cases were the sample could be rescued by re-labeling it to the proper individual. Bcftools gtcheck was used to compare all whole genome sequencing and genotyping data. These data were subsetted to include only dbSNP non-AT/GC SNPs with MAF >0.25.
