For all models (Extended Data Table 1), we applied the following quality control filters: minimum coverage 10X; annotation in CCDS transcripts (release 22; approximately 34 Mb); at most 80% alternate reads in homozygous genotypes; percent of alternate reads in heterozygous variants ≥ 0.25 and ≤ 0.8; binomial test of alternate allele proportion departure from 50% in heterozygous state P > 1 × 10−6; GQ ≥ 20; FS ≤ 200 (indels) ≤ 60 (SNVs); MQ ≥ 40; QUAL ≥ 30; read position rank sum score ≥ −2; MQRS ≥ −8; DRAGEN variant status = PASS; the variant site achieved tenfold coverage in ≥ 25% of gnomAD exomes, and if the variant was observed in gnomAD exomes, the variant achieved exome z-score ≥ −2.0 and exome MQ ≥ 30.
