Low-quality FFPE mode is a specialized setting designed for formalin-fixed paraffin-embedded (FFPE) samples with significant DNA degradation, indicated by a DNA Integrity Number (DIN) score of 2 or lower.
FFPE preservation introduces chemical modifications to DNA that can be mistaken for true somatic variants and inflate false-positive rates:
Deamination events (C>T and G>A changes)
Chimeric reads from cross-linked DNA fragments
When you enable this setting, the pipeline activates additional filtering steps that specifically target FFPE-induced artifacts, increasing the specificity of variant calls. Note that these additional filters may slightly decrease sensitivity for borderline variant calls.
FFPE with DIN > 2
Standard mode
FFPE with DIN ≤ 2
Low-quality FFPE mode
Fresh frozen, blood, cfDNA
Standard mode
You can compare results by running the same sample in both modes.
Tip. If you are unsure, run the sample in standard mode first and check the Supplementary (chimeric) alignments QC metric. If it exceeds 1–2%, rerun in low-quality FFPE mode. See Key QC Metrics.
Last updated
Was this helpful?
Was this helpful?
