> 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/troubleshooting/false-positives.md).

# Unexpected Variant Calls

If you observe unexpected variant calls that you suspect are artifacts, check the following:

## 1. Systematic Noise File

Verify that you provided a **systematic noise file** as input, especially in tumor-only mode.

Confirm that the samples used to build the noise baseline match your tumor samples in:

* **Sample type** (FFPE, fresh frozen, blood)
* **Sample quality** (DIN score range)
* **Library prep kit**

Use **at least 30 samples** for the baseline. See [Stage 1: Generate a Systematic Noise File](/dragen-somatic-for-idt-custom-panels/stage-1-generate-systematic-noise-file/noise-baseline.md) for best practices.

## 2. Chimeric Reads

Check the **Supplementary (chimeric) alignments** QC metric. If the value is elevated above **1–2%**, or above your typical range, consider running the sample in [low-quality FFPE mode](/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/ffpe-mode.md).

***

If none of the above resolves the issue, contact Illumina Technical Support at <techsupport@illumina.com>.


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