The NCTR team’s pipelines were applied on WES1, WES2, and WES3 datasets. Reference genomes were downloaded from Illumina iGenomes website for both hg19 and hg38 version. Reads were aligned with BWA-MEM [29] (v0.7.12-r1039) and Bowtie2 [31] (v2.3.2). Duplicate reads were marked using Picard [56] (v2.7.1) MarkDuplicates function. The reads were then local realigned around small insertions and deletions (indels) and base quality scores were recalibrated using GATK [58] (v3.6-0-g89b7209). dbSNP (b150) was supplied to GATK for indel realignment and quality score recalibration. GATK’s default downsampling option was suspended by setting “--downsampling_type NONE.” Variants were called with FreeBayes [21] (v1.1.0-46-g8d2b3a0) and VarScan2 [61] (v2.4.0) with their default settings.
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