Analysis Output

When the analysis run completes, the DRAGEN TruSight Oncology 500 Analysis Software generates an analysis output folder in a specified location.

To view analysis output, navigate to the analysis output folder and select the files that you want to view.

Metrics Output

The MetricsOutput.tsv file contains the following quality control metrics for all samples:

• DNA library QC metrics for:

  • Small variant calling

  • TMB

  • MSI

  • CNV

  • [HRD] GIS

• RNA library QC metrics

• Run QC metrics, analysis status, and contamination

This TSV file also includes expanded DNA library QC metrics per sample, based on total reads, collapsed reads, chimeric reads, and on-target reads. Analysis using RNA samples also produces RNA library QC metrics and expanded RNA library QC metrics per sample based on total reads and coverage.

The MetricsOutput.tsv file is a final combined metrics report with sample status, key analysis metrics, and metadata. Sample metrics within the report include suggested lower specification limits (LSL) and upper specification limits (USL) for each sample in the run.

For troubleshooting information, refer to [Troubleshooting](ADD LINK TO TROUBLESHOOTING)

Single Node Analysis Output Folder Structure

Single output folder structure is as follows.

• Logs_Intermediates

  • AdditionalSarjMetrics— Contains per pair ID calculations to support the PCT_TARGET_250X metric.

  • Annotation—Contains outputs for small variant annotation.

    • Subfolders per sample ID—Contains the aligned small variants JSON.

• CombinedVariantOutput

  • Subfolders per pair ID—Contains the combined variant output TSV files.

  • A combined output log file.

• Contamination

  • Subfolders per DNA sample ID—Contains the contamination metrics JSON file and output logs.

• DnaDragenCaller

  • Subfolders per sample ID—Contains the aligned BAM and index files, small variant VCF and gVCF, copy number variant VCF, MSI JSON, and QC outputs in CSV format.

• DnaDragenExonCNVCaller

  • Subfolders per DNA sample ID—Contains the exon-level CNV JSON,the supporting calculation, and the QC files.

• DnaFastqValidation—Contains the FASTQ validation output log for DNA samples.

• FastqDownsample

  • Subfolders per RNA sample ID—Contains FASTQ files and output logs.

  • FastqDownsample output

• Gis—Contains GIS-related files for HRD samples.

  • Subfolders per HRD sample ID—Contains the GIS JSON, the supporting calculation, and the QC files.

• LrAnnotation

  • Subfolders per DNA sample ID—Contains the annotated exon-level CNV JSON.

• LrCalculator

  • Subfolders per DNA sample ID—Contains the exon-level CNV VCF.

• MetricsOutput

  • Subfolders per pair ID—Contains the metrics output TSV files.

  • A combined output log file.

• ResourceVerification—Contains the resource file checksum verification logs.

• RnaAnnotation

  • Subfolders per RNA sample ID—Contains the annotated splice variant JSON.

• RnaDragenCaller

  • Subfolders per sample ID—Contains the aligned BAM, fusion candidates CSV, and QC outputs in CSV format.

• RnaFastqValidation—Contains the FASTQ validation output log for RNA samples.

• RnaFusion

  • Subfolders per RNA sample ID—Contains the All Fusions CSV and Fusion Processor logs.

• RnaQcMetrics

  • Subfolders per RNA sample ID—Contains the RNA QC metrics JSON.

• RnaSpliceVariantCalling

  • Subfolders per RNA sample ID—Contains the splice variants VCF.

• Run QC—Contains the Run QC metrics JSON, Intermediate Run QC metrics JSON, and log file.

• SampleAnalysisResults

  • Subfolders per pair ID—Contains the Sample Analysis Results JSON and detailed log file.

  • SampleSheetValidation—Contains the Intermediate sample sheet and validation log.

• Tmb

  • Subfolders per DNA sample ID—Contains the TMB metrics CSV, TMB trace TSV, and related files and logs. passing_sample_steps.json —Contains the steps passed for each sample ID. pipeline_trace.txt—Contains a summary and troubleshooting file that lists each Nextflow task executed and the status (for example, COMPLETED or FAILED). run.log—Contains a complete trace-level log file describing the Nextflow pipeline execution. run_report.html—Contains high-level run statistics (performance, usage, etc.) run_timeline.html —Contains timeline-related information about the analysis run.

• Results

  • Metrics Output TSV (all pair IDs)

• Pair ID—The following outputs are produced for each sample:

  • Combined Variant Output TSV

  • Metrics Output TSV

  • TMB Trace TSV

  • Small Variant Genome VCF

  • Small Variant Genome Annotated JSON

  • Copy Number Variant VCF

  • GIS JSON

  • MSI JSON

  • Exon-level CNV VCF

  • Exon-level CNV Annotated JSON

  • All Fusion CSV

  • Splice Variant VCF

  • Splice Variant Annotated JSON

Multiple Node Analysis Output Folder Structure

Multiple output folder structure is as follows.

• Demultiplex_Output

  • Logs_Intermediates—Contains FASTQ files per sample.

• NodeX_Output—The following outputs are produced for each node used:

  • Logs_Intermediates

  • Results—Contains results only for the samples run on the node.

• Gathered_Output

  • Results—Contains results for all samples from all nodes.