Curated TOSCA Filters (GRCh38)

Curated Systematic Noise and Alu Filter Baselines for nf-core-NEXUS-6 (GRCh38) - TOSCA Overview This dataset provides highly curated, VCF-formatted genomic artifacts designed to filter systematic sequencing noise in tumor-only somatic variant calling workflows. These files are optimized for high-performance querying and serve as native dependencies for the nf-core-NEXUS pipeline. Contents The tosca_somatic_filters_hg38.tar.gz archive contains: WES_Systematic_Noise_hg38.vcf.gz (and .tbi) FFPE_Systematic_Noise_hg38.vcf.gz (and .tbi) Alu_regions_hg38_clean.bed Pipeline Integration & Reproducibility This tarball is designed for direct ingestion by Nextflow workflows. All scripts, Conda environments, and detailed documentation used to generate these VCFs from the raw DRAGEN data are hosted on our GitHub repository: TOSCA Filters Note on Reference Genome: To execute the processing scripts found on GitHub, you must ensure access to a localized GRCh38 .fasta reference genome. The reference file must be downloaded directly into a dedicated reference/ directory within the project root. Intellectual Property and Original Source Disclaimer The raw, unmodified Systematic Noise Baseline (SNB) data and Alu region definitions are the intellectual property of Illumina, Inc. and were originally generated via the DRAGEN™ Bio-IT Platform. The structural modifications provided in this archive (converting pseudo-BED to VCF) are strictly for non-commercial, academic, and research purposes to facilitate allele-specific soft-filtering in open-source architectures. This dataset is not endorsed by or affiliated with Illumina, Inc.