CNV Workflow

The DRAGEN CNV pipeline follows the workflow shown in the following figure.

DRAGEN CNV Pipeline Workflow

This pipeline uses many aspects of the DRAGEN platform available in other pipelines, such as hardware acceleration and efficient I/O processing. To enable CNV processing in the DRAGEN Host Software, set the --enable-cnv command line option to true.

The CNV pipeline has the following processing modules:

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Target Counts—binning of the read counts and other signals from alignments.

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Bias Correction—correction of intrinsic system biases.

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Normalization—detection of normal ploidy levels and normalization of the case sample.

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Segmentation—breakpoint detection via segmentation of the normalized signal.

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Calling / Genotyping—thresholding, scoring, qualifying, and filtering of putative events as copy number variants.

The normalization module can optionally take in a panel of normals (PoN), which is used when a cohort or population samples are readily available. All other modules are shared between the different CNV algorithms.