Variant calling and filtering
Variant calling was performed using the Genome Analysis Toolkit (GATK)
HaplotypeCaller function (version 4.1.2.0). Variant filtering was
performed using GATK VariantFiltration function (version 4.1.2.0)
(Van der Auwera et al., 2013 ). Sequencing data were aligned to
reference genome (version hg38) using BWA (Jo & Koh, 2015 ). In
order to assess the potential functional impacts of variants, five
bioinformatics algorithms were utilized in our study: PolyPhen-2 (PP2),
Sorting Tolerant From Intolerant (SIFT), Meta-support vector machine
(Meta-SVM), megalencephaly-capillary malformation (MCAP), and Mutation
Taster.