Bioinformatics: Variant calling
Variants were called using Clair v2 (Luo et al., 2020) and filter
parameters for variants required >20x coverage, allele
frequency 20-80%, 96% confidence, and allele agreement with the
validated DNM. The remaining variants were error polished using the high
base accurate WES data, removing variants that disagree with any
overlapping WES data. WES data for patients and parents was used in
filtering ONT called variants illustrated in Figure 2 and Supplementary
Tables 4 and 5. Intronic variants identified were further error polished
where the inheritance information was available from long-read parental
data.