Copy Number Variant Calling
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The DRAGEN Copy Number Variant (CNV) Pipeline can call CNV events using next-generation sequencing (NGS) data. This pipeline supports multiple applications in a single interface via the DRAGEN Host Software, including processing of whole-genome sequencing (WGS) data and whole-exome sequencing (WES) data.
The DRAGEN CNV pipeline has two normalization modes of operation (see each pipeline for which of these are supported). The two modes apply different normalization techniques to handle biases that differ based on the application, for example, WGS versus WES. While the default option settings attempt to provide the best trade-off in terms of speed and accuracy, a specific workflow may require more finely tuned option settings.
The following figures show a high-level overview of the steps in the DRAGEN CNV Pipeline as the signal traverses through the various stages. These figures are examples and are not identical to the plots that are generated from the DRAGEN CNV Pipeline.
The first step in the DRAGEN CNV Pipeline is the target counts stage. The target counts stage extracts signals such as read count and improper pairs and puts them into target intervals.
Read Count Signal
Improper Pairs Signal
Next, the case sample is normalized against the panel of normals or against the estimated normal ploidy level. Any other biases are subtracted out of the signal to amplify any event level signals.
Normalization
The normalized signal is then segmented using one of the available segmentation algorithms. Events are then called from the segments.
Segments
Called Events
The events are then scored and emitted in the output VCF.
