> For the complete documentation index, see [llms.txt](https://help.dragen.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.dragen.illumina.com/dragen-v4.5/product-guides/dragen-v4.5/germline/standard-sbs/structural_variants_accuracy.md).

# WGS Structural Variants

Generated on **2026-05-07**

## Structural Variants

The DRAGEN Structural Variant (SV) caller identifies large insertions, deletions and genomic arrangements from mapped DNA reads. For details, refer to the [DRAGEN user guide for structural variant calling](/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/sv-calling.md).

**DRAGEN**: DRAGEN 4.5.4 | **Truthset**: HG002 T2TQ100-v1.1-v0.018 on Truvari v4.2.2 | **Reference**: GRCh38

<details>

<summary>SV WGS historical comparison table (click to expand)</summary>

| Method       | Recall | Precision | F1-score |
| ------------ | ------ | --------- | -------- |
| DRAGEN 4.5.4 | 0.880  | 0.969     | 0.922    |
| DRAGEN 4.4   | 0.807  | 0.963     | 0.878    |
| DRAGEN 4.3   | 0.511  | 0.953     | 0.665    |

</details>

**Comparison with previous DRAGEN versions**

![SV WGS accuracy comparison across DRAGEN versions](https://25033470-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FG9szlFZupV6Q2DasL98y%2Fuploads%2Fgit-blob-268ddc8f1aacf81e37bbaf16e24a1f6052b63b0b%2Fsv_wgs_historical_comparison.png?alt=media)

**Mobile Element Insertions**

The general purpose SV routine can detect Mobile Element Insertions (MEIs) with assembled inserted sequences like other regular insertions. If missed by the general purpose SV routine, MEIs will be rescued by the MEI specific routine based on similarity between assembled contigs and known sequences in the MEI catalog.

Recall for **HG002 NIST v0.6 MEI** (Wittyer v0.5.4.1):

<details>

<summary>SV MEI historical comparison table (click to expand)</summary>

| Method       | Recall |
| ------------ | ------ |
| DRAGEN 4.5.4 | 0.985  |
| DRAGEN 4.4   | 0.906  |
| DRAGEN 4.3   | 0.885  |

</details>

**Comparison with previous DRAGEN versions**

![SV MEI recall trend across DRAGEN versions](https://25033470-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FG9szlFZupV6Q2DasL98y%2Fuploads%2Fgit-blob-fd8b322bce538aa988e35c0d5acec9a5e202eb83%2Fsv_mei_historical_recall.png?alt=media)


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