Analysis Output

Analysis Output

When the analysis run completes, the software generates an analysis output in a specified location with the folder name DRAGEN_WGS_HEME_4.4.4_Analysis_${timestamp}. In ICA, analysis output is listed in the Output section of the analysis, where the folder name is a combination of user reference, pipeline name, and a UUID. Within the analysis folder, each analysis step generates a subfolder within the Logs_Intermediates folder.

Output Folders

This section describes each output folder generated during analysis and where to find metric and analytic files when the pipeline is executed.

• 📂 Results - Contains the final result files from the pipeline.

  • 📄 MetricsOutput.tsv - Contains summary metrics for all samples.

    • 📂 Sample1

    • 📄 Sample1.sv.small_indel_dedup.filtered.vcf.gz — Contains DNA structural variants excluding the indels already present in the hard-filtered.vcf file after applying the DragenSvExtraFilters.

    • 📄 Sample1.hard-filtered.vcf.gz—Contains small variants VCF.

    • 📄 Sample1.cnv.vcf.gz —Contains copy number variants VCF.

    • 📄 Sample1_MetricsOutput.tsv—Contains summary metrics for the specific sample.

    • 📄 Sample1.tn.bw —Contains the BigWig representation of the tangent normalized signal.

    • 📄 Sample1.tumor.baf.bedgraph.gz —Contains the BED graph representation of the B-allele frequency (if available).

• 📂 Logs_Intermediates - Contains all intermediate files for each step of the pipeline.

  • 📂 DragenSvExtraFilters

  • 📂 SampleSheetValidation

  • 📂 ResourceVerification

  • 📂 RunQc(only when started from BCLs)

  • 📂 FastqGeneration (only when started from BCLs)

  • 📂 FastqValidation

  • 📂 DragenCaller

  • 📂 AdditionalSarjMetrics

  • 📂 SampleAnalysisResults

  • 📂 MetricsOutput

  • 📂 passing_sample_steps.json

  • 📂 pipeline_trace.txt

  • 📂 nextflow_work_logs (ICA only)

    • On DRAGEN server, Nextflow logs are contained in the Work folder.

Log Files

All logs in Logs_Intermediates are generated from the running analysis software. Inputs to the running Docker container (for example, the run folder, sample sheet, and FASTQ folder) are mapped from native locations on the server to the following locations in the container:

Input	Running Docker Container Location
Run folder	/opt/illumina/run-folder
Sample sheet	/opt/illumina/SampleSheet.csv
FASTQ folder	/opt/illumina/fastq-folder
Resources	/opt/illumina/resources
Analysis output folder	/opt/illumina/analysis-folder

The paths in the log messages refer to paths within the running docker container, not paths on the server.

File Overview

This section describes the summary output files generated during analysis.

Metrics Output

File name: MetricsOutput.tsv

The metrics output file is a final combined metrics report that provides sample status, key analysis metrics, and metadata in a tab-separated values (TSV) file. Sample metrics within the report indicate guideline-suggested lower specification limits (LSL) and upper specification limits (USL) for each sample in the run. One metrics output file is generated for the entire run. An additional file is generated for each sample.

Run Metrics

Run metrics from the analysis module indicate the quality of the sequencing run. Review the following metrics to assess run data quality:

Metric	Description	Recommended Threshold
PCT_Q30_R1	Percentage of bases with a quality score ≥ 30 from Read 1.	≥ 80.0 (≥85.0 for NovaSeq X Plus)
PCT_Q30_R2	Percentage of bases with a quality score ≥ 30 from Read 2.	≥ 80.0 (≥85.0 for NovaSeq X Plus)

The values in the Run Metrics section are listed as NA in the following situations:

• The analysis was started from FASTQ files.

• The analysis was started from BCL files, and the InterOp files are missing or corrupt.

Sample QC Metrics

Review the following metrics to assess sample data quality:

Metric (UOM)	Recommended Threshold	Description
TUMOR_ESTIMATED_SAMPLE_CONTAMINATION (NA)	NA
TUMOR_MAPPED_READS_PCT (%)	NA
TUMOR_INSERT_LENGTH_MEDIAN (count)	NA
TUMOR_Q30_BASES_EXCL_DUPS_AND_CLIPPED_BASES (bp)	NA
AVERAGE_AUTOSOMAL_COVERAGE_OVER_GENOME (count)	NA
GC_NORMALIZED_COVERAGE_AT_GCS_20_39 (count)	NA
GC_NORMALIZED_COVERAGE_AT_GCS_60_79 (count)	NA