sequencing, variants were filtered for minimum read depth (DP), variant calling confidence score (QD), VQSLOD and mapping and variant quality scores (MQ, GQ). Variant-level QC was performed using PLINK15 which includes checking genotype concordance using previous GWAS data, excluding variants with excess and/or systematic genotype missingness, examining departure from Hardy-Weinberg Equilibrium and identifying Mendelian inconsistencies among related individuals. Variants were annotated using ANNOVAR22. Variants were annotated with population frequencies in existing variant databases including dbSNP, 1000 Genomes, and the Exome Aggregation Consortium (ExAC). Prediction of variant function was obtained from POLYPHEN23 and SIFT24, cross-species conservation scores were obtained from PhyloP25, PhastCons26 and GERP25 and disease association were performed using OMIM27, HGMD28, ClinVar29.
