Analysis Output
When the analysis run completes, the DRAGEN TruSight Oncology 500 ctDNA 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.
Analysis Output Folder Structure
Single output folder structure is as follows.
Logs_Intermediates
AdditionalSarjMetrics
Annotation—Contains outputs for small variant annotation.
Subfolders per sample ID—Contains the aligned small variants JSON.
CombinedVariantOutput
Subfolders per sample ID—Contains the combined variant output TSV files.
A combined output log file.
Contamination
Subfolders per sample ID—Contains the contamination metrics JSON file and output logs.
CoverageReports
DnaFusionFiltering
DragenCaller
Subfolders per sample ID—Contains the aligned BAM and index files, small variant VCF and gVCF, copy number variant VCF, MSI JSON, exon coverage report bed, and QC outputs in CSV format.
FastqValidation—Contains the FASTQ validation output log for the samples.
FastqGeneration
MetricsOutput
Subfolders per sample ID—Contains the metrics output TSV files.
A combined output log file.
ResourceVerification—Contains the resource file checksum verification logs.
Run QC—Contains the Run QC metrics JSON, Intermediate Run QC metrics JSON, and log file.
SampleAnalysisResults
Subfolders per sample ID—Contains the Sample Analysis Results JSON and detailed log file.
SampleSheetValidation—Contains the Intermediate sample sheet and validation log.
Passing Sample Steps - JSON file that contains the steps passed for each Sample ID
Tmb
Subfolders per sample ID—Contains the TMB metrics CSV, TMB trace TSV, and related files and logs.
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 Sample IDs)
Sample 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 VCF
Small Variant Annotated JSON
Copy Number Variant VCF
MSI JSON
Fusions CSV
Exon Coverage Report TSV
Gene Coverage Report TSV
ICA Output Folder Structure
This section describes each output folder generated during analysis and where to find metric and analytic files when the pipeline is executed. The same output folder structure and content exist in ICA and BaseSpace Sequence Hub.
High-Level Folder Structure
Run ID
TSO500_Nextflow_logs
_manifest.json
Results
_tags.json
Logs_intermediates
Errors—This folder is only present when analysis fails
TSO500_Nextflow_logs Folder Structure
The TSO_500_Nextflow_Logs provides information related to the execution of the pipeline on ICA as a whole and for specific nodes (when an analysis is split across multiple nodes). It contains files used to execute parts of the workflow on different nodes as well as records of the nextflow execution on those nodes.
TSO_500_Nextflow_Logs
_manifest.json
Results Folder Structure
Contains the aggregated MetricsOutput.tsv file at the root level. Additionally, the Results folder contains a subfolder for each sample ID.
Results
MetricsOutput.tsv
Sample_1
Sample_2
Sample_<#>
The Results subfolder contains the following files:
Results
MetricsOutput.tsv
<Sample_id>
CombinedVariantOutput.tsv
Fusions.csv
tmb.trace.tsv
hard-filtered.gvcf
hard-filtered.vcf
SmallVariants_Annotated.json.gz
cnv.vcf
exon_cov_report.tsv
gene_cov_report.tsv
MetricsOutput.tsv
microsat_output.json
Logs_intermediates Folder Structure
Contains folders for each submodule in the DRAGEN TSO 500 ctDNA on ICA pipeline. The folders contain a copy of all the relevant files required to create the metric output files and report files, as well as the combined log files at the root level and subfolders for each sample.
Logs_intermediates
AdditionalSarjMetrics
Annotation
CombinedVariantOutput
Contamination
CoverageReports
DnaFusionFiltering
DragenCaller
FastqValidation
FastqGeneration
MetricsOutput
PassingSampleSteps
ResourceVerification
Run QC
SampleAnalysisResults
SampleSheetValidation
Tmb
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:
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.
Errors Folder Structure
Contains Errors.tsv. This file contains the summary of all the errors encountered during pipeline execution.
Errors
Errors.tsv
NovaSeq 6000Dx Analysis Application Output Folder Structure
The following files and folders are created during analysis by NovaSeq 6000Dx Analysis Application:
analysisResults.json
CopyComplete.txt
edgeos.nextflow.config
inputs/
sampleMapping.json
SampleSheet.csv
SampleSheet.json
Logs_Intermediates
Manifest.tsv
params.json
Results/
workflowLogs/
nf-main-***.log
When the analysis run completes, the analysis application generates an analysis output in a specified location. To view analysis output, follow the steps below:
On the “Completed” runs tab, select the run
Review the run details page, and this will give the information to access the output folder
External Location: is the input for the run
Analysis Output Folder: is where the output is stored. To navigate to this page, follow the “server location” and the gds analysis output folder
Navigate to the directory that contains the analysis output folder
Open the folder, and then select the files that you want to view
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