Documentation / Getting Started / Quality Presets
Quality Presets
Quality filtering occurs before annotation and classification. Three configurable presets control the stringency of variant filtering based on sequencing quality metrics.
| Preset | Quality (QUAL) | Depth (DP) | Genotype Quality (GQ) | Recommended Use |
|---|---|---|---|---|
| Strict | >= 30 | >= 20 | >= 30 | High-confidence clinical reporting |
| Balanced | >= 20 | >= 15 | >= 20 | Standard clinical analysis (default) |
| Permissive | >= 10 | >= 10 | >= 10 | Maximum sensitivity / research |
When to Use Each Preset
Strict
Use for final clinical reports where only high-confidence variant calls are acceptable. Minimizes false positives at the cost of potentially missing variants in low-coverage regions.
Balanced
Recommended for most clinical analyses. Provides a good balance between sensitivity and specificity. This is the default preset.
Permissive
Use in research settings, for reanalysis of older or lower-quality sequencing data, or in cases where maximum sensitivity is needed even at the cost of more false positives. Review flagged variants carefully.
ClinVar Rescue Mechanism
Regardless of the selected preset, variants with documented ClinVar Pathogenic or Likely Pathogenic significance that fail quality thresholds are not discarded. They are flagged as "rescued" variants and proceed through the full classification pipeline. This prevents clinically significant findings from being silently excluded due to sequencing quality in low-coverage regions.
When reviewing rescued variants, pay careful attention to the quality metrics. Low sequencing coverage means the genotype call itself may be unreliable. Consider confirmation by Sanger sequencing for rescued variants that are clinically actionable.
For the complete quality filtering documentation with technical details, see the Methodology page.