We evaluated the genotypes provided by Fawkes of autosomal SNPs across a set of 790 ancestrally diverse samples. Across these samples (comprising 689,451,960 total genotypes) Fawkes changed 717,301 SNP genotypes in 267,070 unique SNPs as compared to running Birdseed alone. A small fraction of SNPs (5,600) had a copy-variable call in at least 1% of unrelated individuals. In the 91 parent-offspring trios available in this dataset, Birdsuite genotypes showed a lower rate of mendelian inconsistencies versus those from Birdseed alone (Table 1). In fact, every family analyzed showed a lower rate of mendelian inheritance errors, with an average decrease of 5% and a maximum decrease of 45% (Fig. 3f). This indicates that copy number variation is an infrequent but not insubstantial source of apparent mendelian inconsistency in all samples, and a major contributor in select samples (potentially owing to cell line artifacts that affect whole chromosomes). As expected, the rate of mendelian inconsistency was particularly reduced across the 11,256 SNPs that lie within common CNPs6, with an average reduction of 33% (Fig. 3e).
