Illumina DRAGEN Baseline Filters for hg38 Exome Analysis (nf-NEXUS Pipeline Extract)

This dataset contains targeted genomic baseline filters extracted from the official Illumina DRAGEN Reference Collections. These specific files are provided to ensure full reproducibility and seamless execution of the nf-NEXUS somatic variant calling pipeline without requiring users to download multi-gigabyte tarballs. Contents: WES_hg38_v2.0.0_systematic_noise.snv.bed.gz: Systematic noise baseline trained on mixed FF/FFPE Whole Exome Sequencing (WES) data. Used for the GATK VariantFiltration step to mitigate platform-specific optical and chemical artifacts. hg38-ht_mask_bed-v4.bed: Hash Table mask bed for hg38. Used in the GATK Mutect2 -XL argument to exclude centromeres, highly homologous regions, and pseudogenes, drastically reducing the False Discovery Rate (FDR) in Tumor-Only analyses.