# 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 . --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/troubleshooting/false-positives.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.