Analysis Output
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When the analysis run completes, the software generates an analysis output in a specified location with the folder name /staging/DRAGEN_Solid_WGS_Tumor_Normal_Pipeline_{version}_Analysis_{datetimestamp}. 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.
Results - Contains the final result files from the pipeline.
MetricsOutput.tsv - Contains summary metrics for all samples.
Case1
Case1_MetricsOutput.tsv - Contains summary metrics for tumor and normal samples for Case1.
TumorSample1
TumorSample1.hard-filtered.vcf.gz - Contains somatic small variant calls.
TumorSample1.cnv.vcf.gz - Contains somatic copy number variant calls.
TumorSample1.sv.vcf.gz - Contains somatic structural variant calls.
TumorSample1_SNV_Tumor_Annotated.json.gz - Contains somatic small variant annotations.
TumorSample1_CNV_Tumor_Annotated.json.gz - Contains somatic copy number variant annotations.
TumorSample1_SV_Tumor_Annotated.json.gz - Contains somatic structural variant annotations.
TumorSample1.tmb.metrics.csv - Contains the TMB result and metrics.
TumorSample1.microsat_output.json - Contains the MSI result and metrics.
This section describes the summary output files generated during analysis.
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 case.
Metric (UOM)
LSL Guideline
USL Guideline
TOTAL_INPUT_READS (Count)
NA
NA
PCT_MAPPED_READS (%)
90.00
NA
PCT_PROPERLY_PAIRED_READS (%)
90.00
NA
PCT_Q30_BASES (%)
80.00
NA
PCT_SOFT_CLIPPED_BASES_R1 (%)
NA
10.0
PCT_SOFT_CLIPPED_BASES_R2 (%)
NA
10.0
PCT_SUPPLEMENTARY_(CHIMERIC)_ALIGNMENTS (%)
NA
15.0
ESTIMATED_READ_LENGTH (bp)
NA
NA
MEAN_INSERT_LENGTH (bp)
NA
NA
MEDIAN_INSERT_LENGTH (bp)
NA
NA
INPUT_BASES_OVER_REFERENCE_GENOME_SIZE (Count)
NA
NA
ESTIMATED_SAMPLE_CONTAMINATION (%)
NA
2.00
Metric (UOM)
LSL Guideline
USL Guideline
PCT_DUPLICATE_MARKED_READS (%)
NA
20.00
PCT_READS_WITH_VALID_OR_CORRECTABLE_UMIS (%)
NA
NA
PCT_READS_IN_DISCARDED_FAMILIES (%)
NA
NA
PCT_READS_FILTERED_OUT (%)
NA
NA
PCT_READS_WITH_UNCORRECTABLE_UMIS (%)
NA
NA
TOTAL_NUMBER_OF_FAMILIES (Count)
NA
NA
FAMILIES_DISCARDED (Count)
NA
NA
DUPLEX_FAMILIES (Count)
NA
NA
MEAN_FAMILY_DEPTH (Count)
NA
NA
Metric (UOM)
LSL Guideline
USL Guideline
AVERAGE_GENOME_COVERAGE (Count)
20.00
NA
PCT_UNIFORMITY_OF_COVERAGE_OVER_20PCT_OF_MEAN (%)
50.00
NA
PCT_GENOME_20X (%)
80.00
NA
Metric (UOM)
LSL Guideline
USL Guideline
TOTAL_INPUT_READS (Count)
NA
NA
PCT_MAPPED_READS (%)
90.00
NA
PCT_PROPERLY_PAIRED_READS (%)
90.00
NA
PCT_Q30_BASES (%)
80.00
NA
PCT_SOFT_CLIPPED_BASES_R1 (%)
NA
10.0
PCT_SOFT_CLIPPED_BASES_R2 (%)
NA
10.0
PCT_SUPPLEMENTARY_(CHIMERIC)_ALIGNMENTS (%)
NA
15.0
ESTIMATED_READ_LENGTH (bp)
NA
NA
MEAN_INSERT_LENGTH (bp)
NA
NA
MEDIAN_INSERT_LENGTH (bp)
NA
NA
INPUT_BASES_OVER_REFERENCE_GENOME_SIZE (Count)
NA
NA
ESTIMATED_SAMPLE_CONTAMINATION (%)
NA
2.00
Metric (UOM)
LSL Guideline
USL Guideline
PCT_DUPLICATE_MARKED_READS (%)
NA
20.00
PCT_READS_WITH_VALID_OR_CORRECTABLE_UMIS (%)
NA
NA
PCT_READS_IN_DISCARDED_FAMILIES (%)
NA
NA
PCT_READS_FILTERED_OUT (%)
NA
NA
PCT_READS_WITH_UNCORRECTABLE_UMIS (%)
NA
NA
TOTAL_NUMBER_OF_FAMILIES (Count)
NA
NA
FAMILIES_DISCARDED (Count)
NA
NA
DUPLEX_FAMILIES (Count)
NA
NA
MEAN_FAMILY_DEPTH (Count)
NA
NA
Metric (UOM)
LSL Guideline
USL Guideline
AVERAGE_GENOME_COVERAGE (Count)
20.00
NA
PCT_UNIFORMITY_OF_COVERAGE_OVER_20PCT_OF_MEAN (%)
50.00
NA
PCT_GENOME_20X (%)
80.00
NA
Metric (UOM)
LSL Guideline
USL Guideline
OUTLIER_BAF_FRACTION (NA)
NA
0.90
Metric (UOM)
LSL Guideline
USL Guideline
ESTIMATED_PURITY (%)
20.00
NA
TumorSample1.hrdscore.csv - Contains the HRD result and metrics.
TumorSample1.tn.bw - Contains tangent normalized somatic coverage in BigWig format.
TumorSample1.tumor.baf.bedgraph.gz - Contains somatic b-allele frequency in BedGraph format.
TumorSample1.bam - Contains aligned somatic reads in BAM format.
TumorSample1.bam.bai - Contains index of aligned somatic reads in BAI format.
NormalSample1
NormalSample1.hard-filtered.vcf.gz - Contains germline small variant calls.
NormalSample1.cnv.vcf.gz - Contains germline copy number variant calls.
NormalSample1.sv.vcf.gz - Contains germline structural variant calls.
NormalSample1.repeats.vcf.gz - Contains germline short tandem repeat calls.
NormalSample1.vntr.vcf.gz - Contains germline variable number tandem repeat calls.
NormalSample1.targeted.vcf.gz - Contains germline targeted (star allele) calls.
NormalSample1.targeted.json - Contains germline targeted (star allele) data in JSON format.
NormalSample1_SNV_Normal_Annotated.json.gz - Contains germline small variant annotations.
NormalSample1_CNV_Normal_Annotated.json.gz - Contains germline copy number variant annotations.
NormalSample1SV_Normal_Annotated.json.gz - Contains germline structural variant annotations.
NormalSample1.hla.tsv - Contains germline HLA typing calls.
NormalSample1.bam - Contains aligned germline reads in BAM format.
NormalSample1.bam.bai - Contains index of aligned germline reads in BAI format.
Logs_Intermediates - Contains all intermediate files for each step of the pipeline (BAMs moved to the Results folder).
ResourceVerification
SampleSheetValidation
NormalFastqValidation
TumorFastqValidation
DragenCaller
TumorNormalVariantCaller
Tmb
Annotation
SampleAnalysisResults
AdditionalSarjMetrics
MetricsOutput
Work - (DRAGEN server only) Contains information and files related to Nextflow execution.