Whole genome sequencing was performed by MedGenome (CA, USA) using the HiSeq X Ten platform (Illumina, USA) utilizing a 150 base-pair (bp) paired-end protocol. The raw FASTQ files were evaluated using FastQC software (Babraham Institute, UK). A proprietary WGS data processing pipeline was designed to process NGS data in automated mode from raw FASTQ files to finalized genotyping data. The pipeline implemented adapter trimming using Trimmomatic [9], BWA MEM [10] alignment to the GRCh38 build of the human genome, duplicate reads marking by Picard (Broad Institute, USA), filtering of the resulting SAM/BAM files via SAMtools [11, 12]. It also utilized GATK tools (Broad Institute, USA) to perform base quality score recalibration (BQSR), genotype calling and variant quality score recalibration (VQSR). GATK VariantAnnotator and BCFtools were employed to perform variant annotation. The pipeline implemented several hard filtering procedures resulting in a final VCF output with all variant and non-variant sites which passed quality control of the filtering step. The pipeline was designed in compliance with GATK Best Practices recommendations for NGS data processing. Single nucleotide variants (SNVs) and indels were called
