Deep whole-exome sequencing of reference sample NA12878 (HG001) on three sequencing platforms
Whole-exome sequencing (Agilent SureSelect Human All Exon V6, PE150) of a single aliquoted genomic DNA sample from the GIAB reference cell line NA12878 (GM12878), sequenced in parallel on three platforms: Illumina NovaSeq 6000, BGI DNBSEQ-T7 and GeneMind SURFSeq 5000. All libraries were prepared from the same DNA stock with the same capture kit, reaching a mean on-target depth of 627 to 742x. The dataset supports benchmarking of germline variant-calling pipelines: depth titration by downsampling to a defined on-target coverage grid, cross-platform comparison, caller comparison (GATK4 HaplotypeCaller vs DeepVariant), reference-build comparison (GRCh38 and GRCh37), and CPU-versus-GPU (NVIDIA Parabricks) concordance, all evaluated against the GIAB HG001 v4.2.1 benchmark.