Resource Files

Distributed as a BaseSpace Project and an ICA Bundle

Product files to support the analysis of samples prepared with the Illumina FFPE DNA Prep with Exome 2.5 Enrichment are distributed as a BaseSpace Project and an ICA Bundle. Please reach out to your local sales representative to get access. Note that these product files are considered early access and will be superseded by official resource files published on the DRAGEN Resources page.

Resource	Prebuilt	Custom
Target BED	If no spike-in probes were included in enrichment, download from Illumina DNA Prep with Exome 2.5 BED files for hg19 or hg38 reference genomes.	If other spike-in probes were included in enrichment, use a BED file of the combined coverage areas, ie., Exome 2.5 Plus Panel and the custom panel. The requirements of a BED file are defined here.
Systematic noise files: considered essential for reducing false positive calls in Tumor-Only workflows, and they are also effective at improving precision in Tumor-Normal workflows.	Prebuilt systematic noise BED files can be downloaded on DRAGEN Resources. The WES_*_v2.0.0_systematic_noise.snv.bed.gz noise files are built from a mixture of FF (fresh-frozen) and FFPE samples, with a mix of TruSeq PCR prep and Nextera prep. Reference genome builds (the * in the file name) include hg19 and hg38.	For instructions on how to build your own systematic noise file using internally-sequenced normal samples, see Custom Systematic Noise Files. The normal samples used to generate the systematic noise file should match as closely as possible the sequencer, sample type, and library prep of the tumor samples. Also available is the DRAGEN Baseline Builder App on BSSH.
CNV - Somatic pipelines: A Panel of normals (PONs) is used for calling gene amplification in tumor samples	Provided in the BSSH project/ICA bundle are the individual target.counts files (i.e. one per normal sample) and combined target.count files. The PON was generated from 45 FFPE benign adjacent samples from different tissue types and from male and female donors with the Illumina FFPE DNA Prep with Exome 2.5 Enrichment protocol. Libraries were sequenced on the NovaSeq 6000 sequencing system. Current supported builds include hg19 and hg38, both target.counts and gc-corrected.target.counts.	As with the systematic noise file, internally-sequenced normal samples can be used to generate a PON. The input should be the UMI-collapsed BAM files of the normal samples, and the reference genome and target BED need to match those used throughout the workflow. Also available are the DRAGEN Baseline Builder App on BSSH and the DRAGEN CNV Baseline Builder 4-3-6 Pipeline on ICA.
MSI - Reference directory of normals: To be used when enabling the biomarker MSI in Tumor-only mode. This is a reference directory containing the miscrosatellite repeat distribution in a collection of normals	A collection of 44 .dist files from benign adjacent samples from different tissue types and from male and female donors with the Illumina FFPE DNA Prep with Exome 2.5 Enrichment protocol. Libraries were sequenced on the NovaSeq 6000 sequencing system. Current supported builds include hg19 and hg38.	See the DRAGEN manual for instructions on how to generate your own reference directory from interally-sequenced normal samples. Also available are the DRAGEN Baseline Builder App on BSSH and the DRAGEN MSI Baseline Builder 4-3-6 Pipeline on ICA.
MSI - Microsatellite sites: list of microsatellite sites from which to calculate instability	An updated list of WES microsatellite sites, will be released with DRAGEN v4.4.	See the DRAGEN manual for how to generate custom microsatellite lists.