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The FASTQ files from the WES1 dataset are quality checked with FastQC [59] to ensure the sequencing quality. Adapters were trimmed using AlienTrimmer [60]. The reads were then mapped to reference genome hg38 and hg19 with bwa-mem [29] (v0.7.12 (RSSMSN01-RSSMSN04)). Samtools [24] fixmate tool was applied to correct any read-pairing issues that may be introduced by bwa. Duplicated reads were marked with Picard [56] MarkDuplicates, and base quality score was recalibrated with GATK [58] BaseRecalibrator and ApplyBQSR. The processed BAM files were then supplied to four variant callers, i.e., GATK mutect2 (v2.1-beta/v 4.0 alpha), Vardict (v1.5.1), samtools mpileup (v1.2), and Sentieon TNscope [25] (201,704.03).

For the WES1, WES2 and WES3 datasets run with the RSSMSN05 and RSSMSN06 pipelines, a similar analysis was performed, but the mapping step to hg38 was done with bwa-mem [29] (v0.7.17). The processed BAM files were supplied to GATK [58] mutect2 (v 4.0.6.0) using default settings and GATK HaplotypeCaller (v 4.0.6.0) for variant calling.

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