CNV-Mag A tool to visualize CNV Events in WGS Data. CNV-Mag is taking use of BAM and short variant VCF files to visualize CNV events in WGS data in simple and direct way. It can help you to verify if a CNV event is real or not. This tool is part of the Broad Clinical Labs's CNV reporting workflow. Background Verifying CNV events can be challenging, especially for multi-megabase events. A common approach involves using IGV to inspect read depth, soft clips, and SNP Allele Fraction (AF). However, this becomes impractical for large events. CNV-Mag addresses these challenges by providing a streamlined tool for visualizing CNV events. It also integrates Samplot, an excellent package for structural variant visualization, as part of its workflow. Workflow CNV-Mag takes BAM and short variant VCF files to visualize CNV events in WGS data. The workflow is shown below: Input: BAM file and BAM index file Aligned BAM file of your sample HG001 BAM file preferred using the same pipeline as above HG002 BAM file preferred using the same pipeline as above Short variant VCF file (Requires AF field in the INFO column) Short variant VCF file of your sample HG001 VCF file preferred using the same pipeline as above HG002 VCF file preferred using the same pipeline as above CNV region (Bed or a list of Strings) Can be a single CNV region or multiple CNV regions Reference genome (hg19 or hg38) There are three main workflows in CNV-Mag: Mag-SNP Visualize all the PASS SNP AF of the CNV region. Mag-Depth Visualize the read depth of the CNV region. Samplot Visualize the discordant reads and split-read signals of the CNV region. Running CNV-Mag on Terra You can run CNV-Mag on Terra. The workflow is available at https://dockstore.org/workflows/github.com/broadinstitute/CNV-Mag/CNV-Mag:dev?tab=info. You can deploy the workflow to your workspace and run it on Terra. Runtime specification CNV-Mag is part of Broad Clinical Lab CNV reporting workflow. The run cost is less than $2 per run.