Structural Variant Calling

The DRAGEN Structural Variant (SV) Caller integrates and extends Manta structural variant calling to provide SV and indel calls 50 bases or larger. SVs and indels are called from mapped paired-end sequencing reads. The SV caller is optimized for analysis of diploid germline variation in small sets of individuals .

The SV caller performs the following actions:

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Discovers, assembles, and scores large-scale SVs, medium-sized indels, and large insertions within a single efficient workflow.

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Combines paired and split-read evidence during SV discovery and scoring to improve accuracy, but does not require split-reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence otherwise.

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Scores known SV deletions and insertions from an input VCF file against one or more input samples, either as a standalone procedure or together with standard SV discovery.

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Provides scoring models for germline variants in small sets of diploid samples .

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Small tandem duplication normalization is performed, and are converted into insertions. As a result some variants may not have a gnomeAD annotations when custom annotation is used.

All SV and indel inferences are output in VCF 4.1 format.