Sample QC

DRAGEN TruSight Oncology 500 ctDNA uses QC metrics to assess the validity of analysis for DNA libraries that pass contamination quality control. The metrics are available in the MetricsOutput.tsv file, refer to Metrics Output for details.

Metric	Description	Recommended Guideline Quality Threshold	Variant Class
CONTAMINATION_SCORE	The contamination score is based on VAF distribution of SNPs.	≤ 1227	All
MEDIAN_EXON_COVERAGE	Median exon fragment coverage across all exon bases.	≥ 1300	Small variant, TMB, Fusion, MSI
PCT_EXON_1000X	Percent exon bases with 1000x fragment coverage.	≥ 80.0	Small variant, TMB
GENE_SCALED_MAD	The median of absolute deviations normalized by gene fold change.	≤ 0.059*	CNV
MEDIAN_BIN_COUNT_CNV_TARGET	The median raw bin count per CNV target.	≥ 6.0	CNV

*The recommended threshold of 0.059 for GENE_SCALED_MAD only applies to real cell‑free DNA.

For troubleshooting information, refer to Troubleshooting