DRAGEN SV Caller Capabilities

The Consumable Prefix SV Caller can discover all structural variant types that are identifiable in the absence of copy number analysis and large-scale de novo assembly. For more information on detectable types, see Detected Variant Classes.

For each structural variant and indel, the SV Caller attempts to assemble the breakends to base pair resolution and report the left-shifted breakend coordinate (per the VCF 4.1 SV reporting guidelines), together with any breakend homology sequence and/or inserted sequence between the breakends. It is often the case that the assembly will fail to provide a confident explanation of the data. In this case, the variant is reported as IMPRECISE, and scored according to the paired-end read evidence only.

You can provide known SVs to be scored as input. This known SV input can be scored either standalone or together with the standard SV discovery workflow, in which case the known and discovered SVs are merged.

The sequencing reads provided as input to the SV Caller are expected to be from a paired-end sequencing assay that results in an "innie" orientation between the two reads of each sequence fragment, each presenting a read from the outer edge of the fragment insert inward.

The SV Caller is primarily tested for whole-genome and whole-exome (or other targeted enrichment) sequencing assays on DNA. For these assays the following applications are supported:

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Joint analysis of 10 or fewer diploid individuals

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Subtractive analysis of a matched tumor/normal sample pair

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Analysis of an individual tumor sample

For joint analysis, there is no specific restriction against larger cohorts, but this has not been extensively tested so there might be stability or call quality issues.

Tumor samples can be analyzed without a matched normal sample. In this case, no scoring function is available, but the supporting evidence counts are available and many filters can still be usefully applied.