Supplemental CNV analysis using DRAGEN Enrichment

Overview and Prerequisites

This page describes use of DRAGEN Enrichment analysis to extend TSO 500 to additional genomic targets captured with spiked-in probes. Specifically, it describes the parameters necessary for CNV analysis. For general DRAGEN Enrichment app usage, input requirements, and supported references, refer to DRAGEN Enrichment BSSH App Support.

This workflow has been tested on DRAGEN Enrichment 4.4.4 and 4.4.6 (with TSO 500 data that includes coverage from MTAP spike-in add-on probes) and produces the same results using both versions. Input requirements are:

1. FASTQ files from a completed TSO 500 analysis or independently run BCL Convert pipeline

2. The resource files discussed below, such as those provided for MTAP spike-in, and/or self generated (such as your own panel of normals (PON), which can be generated using this app; best practices are discussed here).

Instructions for Running on BSSH

Launch the DRAGEN Enrichment BSSH App 4.4.6 and configure as indicated below and with the appropriate resource files (for instance, those for MTAP spike-in). For all other app fields, use DRAGEN Enrichment defaults.

DRAGEN Enrichment Settings

Parameter	Selection
Input FASTQs	Attach the same FASTQ files used for (or generated by) TSO 500 analysis
Variant Caller Mode	Somatic
Reference	Select the reference that matches the spike-in resource bundle (e.g., for MTAP spike-in, Homo Sapiens [NCBI] hs37d5 with chr prefix v5)
Targeted Regions	Custom BED
Custom Target BED File	Provide the bed file for the regions targeted by the spiked-in probes, including any targeted control sequences
Systematic Noise Filter (under Somatic Variant Calling)	Uncheck
Duplicate Marking (under Advanced Settings)	Uncheck
Additional DRAGEN Command-line Arguments	Check the acknowledgement and enter command-line arguments as specified in the resource bundle. Note that this field accepts command-line arguments without verification of correctness or applicability.
Additional Resource File	Provide additional resource files as necessary for the supplementary analysis. For MTAP spike-in, for instance, this includes the target BED file, BED files for QC and for segment mean calling boundaries, and a panel of normals counts file.

Running DRAGEN Enrichment on Local DRAGEN Server

See specific resource pages, such as for MTAP spike-in, for full command line arguments.