> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/ffpe-mode.md).

# Low-Quality FFPE Mode

Low-quality FFPE mode is a specialized setting designed for formalin-fixed paraffin-embedded (FFPE) samples with significant DNA degradation, indicated by a DNA Integrity Number (DIN) score of **2 or lower**.

## Why FFPE Samples Need Special Handling

FFPE preservation introduces chemical modifications to DNA that can be mistaken for true somatic variants and inflate false-positive rates:

* **Deamination events** (C>T and G>A changes)
* **Chimeric reads** from cross-linked DNA fragments

## What Low-Quality FFPE Mode Does

When you enable this setting, the pipeline activates additional filtering steps that specifically target FFPE-induced artifacts, increasing the **specificity** of variant calls. Note that these additional filters may slightly **decrease sensitivity** for borderline variant calls.

## How to Decide

| Sample profile             | Recommended mode      |
| -------------------------- | --------------------- |
| FFPE with DIN > 2          | Standard mode         |
| FFPE with DIN ≤ 2          | Low-quality FFPE mode |
| Fresh frozen, blood, cfDNA | Standard mode         |

You can compare results by running the same sample in both modes.

{% hint style="info" %}
**Tip.** If you are unsure, run the sample in standard mode first and check the **Supplementary (chimeric) alignments** QC metric. If it exceeds 1–2%, rerun in low-quality FFPE mode. See [Key QC Metrics](/dragen-somatic-for-idt-custom-panels/qc-and-interpretation/qc.md).
{% endhint %}


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