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 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.

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If none of the above resolves the issue, contact Illumina Technical Support at [e-mail].