> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen/dragen-v4.6/product-guides/dragen-v4.6/qc-metrics.md). # DRAGEN QC Metrics DRAGEN generates multiple pipeline-specific metrics including: * Mapping and Aligning metrics * Variant calling metrics * Biomarker metrics * Coverage (or enrichment) metrics and reports * Duration (or run time) metrics Figure 10: Generation of Metrics and Reports ![](https://400428970-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FS6tWlZO1JqcbWYgnhR2X%2Fuploads%2Fgit-blob-b9858b6cd923766fc439ad83f88a19516828de5c%2Fqc-metrics-reporting.GenerationOfMetricAndReports.png?alt=media) DRAGEN QC metrics are available in two output formats: **JSON Format (recommended)**: All metrics are available in a unified JSON file for programmatic access. See [JSON Metrics Reporting](/dragen/dragen-v4.6/product-guides/dragen-v4.6/qc-metrics/json-metrics-reporting.md) for details. **CSV Format**: Individual CSV files are written to the run output directory: * \.mapping\_metrics.csv * \.vc\_metrics.csv * \.\\_coverage\_metrics.csv * \.time\_metrics.csv * \.\.csv Each CSV includes 5 columns: Section, Subsection (e.g. read group or sample), Metric, Value 1 (Count/Ratio/Minutes) and Value 2 (Percentage/Seconds). ## Getting Started For a quick QC checklist with critical metrics and success criteria, see [Minimal Checklist](/dragen/dragen-v4.6/product-guides/dragen-v4.6/qc-metrics/minimal-checklist.md). For comprehensive metric documentation by topic, see the sections below. ## Metrics Documentation Overview DRAGEN produces metrics across multiple pipeline stages. Detailed metrics documentation is organized by topic below. ### QC Metrics (detailed below) * [**Mapping and Alignment Metrics**](/dragen/dragen-v4.6/product-guides/dragen-v4.6/qc-metrics/mapping-metrics.md): Read quality, MAPQ distribution, pairing, clipping, insert size, contamination * [**Coverage and Callability Metrics**](/dragen/dragen-v4.6/product-guides/dragen-v4.6/qc-metrics/coverage-metrics.md): Depth, uniformity, callability across genome/target regions, custom BED regions * [**GC Bias Metrics**](/dragen/dragen-v4.6/product-guides/dragen-v4.6/qc-metrics/gc-bias-metrics.md): Coverage by GC content, dropout analysis * [**Duration Metrics**](/dragen/dragen-v4.6/product-guides/dragen-v4.6/qc-metrics/duration-metrics.md): Pipeline stage timing and performance * **Somatic Callable Regions**: See [Coverage and Callability Metrics](/dragen/dragen-v4.6/product-guides/dragen-v4.6/qc-metrics/coverage-metrics.md#somatic-callable-regions-report) ### Pipeline-Specific Metrics (other sections) * **Small Variant Calling Metrics**: SNP/indel counts, Ti/Tv ratios, het/hom ratios, callability. See [Small Variant Calling Metrics](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-dna-pipeline/small-variant-calling/small-variant-calling-metrics.md) * **Somatic Variant Caller Metrics**: Germline tagging in tumor-only mode, allele transition noise. See [Somatic Mode](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-dna-pipeline/small-variant-calling/somatic-mode.md) * **CNV Metrics**: Copy number variant counts, tumor purity, ploidy. See [CNV Germline](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-dna-pipeline/cnv-overview/cnv-germline.md), [CNV Somatic](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-dna-pipeline/cnv-overview/cnv-somatic.md) * **SV Metrics**: Structural variant counts by type. See [SV Calling](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-dna-pipeline/sv-calling.md) * **Biomarker Metrics**: * TMB (Tumor Mutational Burden). See [Biomarker TMB](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-dna-pipeline/biomarkers/biomarker-tmb.md) * MSI (Microsatellite Instability). See [Biomarker MSI](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-dna-pipeline/biomarkers/biomarker-msi.md) * HRD (Homologous Recombination Deficiency). See [Biomarker HRD](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-dna-pipeline/biomarkers/biomarker-hrd.md) * **RNA Quantification Metrics**: Gene/transcript expression, strand bias. See [Gene Expression Quantification](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-rna-pipeline/gene-expression-quantification.md) * **RNA Fusion Metrics**: Gene fusion candidates. See [Gene Fusion Detection](/dragen/dragen-v4.6/product-guides/dragen-v4.6/dragen-rna-pipeline/gene-fusion-detection.md) --- # Agent Instructions This documentation is published with GitBook. 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