# Missed Variant Calls

If an expected variant is not reported in the VCF output, check the following in order:

## 1. Coverage Overall

Check the **Average alignment coverage over target region** QC metric. Coverage of **150x–200x or higher** is typically required for sensitivity down to 5% VAF. If coverage is low, consider:

* Deeper sequencing on the affected sample
* Repeating library preparation with increased input DNA

## 2. Coverage at Position

Check coverage at the specific genomic position where the variant was expected:

* **If the variant appears in the VCF:** Check the `DP` field for the read depth at that position.
* **If the variant is missing from the VCF:** Visualize the BAM file in a genome browser such as IGV (Integrative Genomics Viewer) to inspect the position directly.

Position-level coverage **above 100x** is typically required for sensitivity at 5% VAF.

## 3. Low-Quality FFPE Mode

If you ran the sample in [low-quality FFPE mode](/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/ffpe-mode.md), try rerunning it as a standard solid sample. The FFPE filters increase specificity but may slightly reduce sensitivity for borderline calls.

***

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


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