GATK CNV Somatic Pair workflow is used for detecting copy number variants (CNVs) as well as allelic segments in a single sample.
Common Use Cases
The workflow denoises case sample alignment data against a panel of normals (PON), created by GATK CNV Panel Workflow, to obtain copy ratios and models segments from the copy ratios and allelic counts. The latter modeling incorporates data from a matched control sample. The same workflow steps apply to targeted exome and whole genome sequenci
This is a companion discussion topic for the original entry at github.com/sevenbridges-openworkflows/Broad-Best-Practice-Somatic-CNV-Workflows/GATK-Somatic-CNV-Pair-Workflow