Reference genome hg38 was used for all work. Reads were mapped with BWA [29] (v0.7.12-r1039). Variants were called with Sentieon Haplotyper (v201611.02). CNV estimation from WGS data was done with Breakdancer [73] (v1.1), CNVnator [74] (v0.3.3), Delly2 [75], DWAC-Seq(v0.7), GenomeSTRiP [76] (v2.0), Meerkat [77](v0.189), MetaSV [78] (v0.5.2), read depth (v0.9.8.4), svclassify [79], and Pindel [80] (v0.2.0). CNV estimation for the WES datasets was performed with CNVkit [81] (v0.8.5), CODEX [82] (v1.6.0), CopywriteR [83] (v2.6.0), DeAnnCNV [84], EXCAVATOR2 [85] (v1.1.2), ExomeDepth [86] (v1.1.10), GATK [58] 4 Alpha, RefCNV [87], SAAS-CNV [88] (v0.3.4), and VarScan2 [61] (v2.4.2). All results were output as VCF files.
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