> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/connected-insights/configure/configuration/du-introduction/du-supported-pipelines/dragen-trusight-oncology-500-analysis-software-v2.6.0-with-hrd.md).

# DRAGEN TruSight Oncology 500 Analysis Software v2.6.0 (with HRD)

```
pipeline:
  type: TSO500
  successMarkerFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv
  failureMarkerFile: "failure.txt"

sampleSheet:
  filePath: SampleSheet.csv
  filePathList:
    - inputs/SampleSheet.csv
    - SampleSheet.csv
  dataHeaderRowMarker: 
    - "[TSO500S_Data]"
    - "[Cloud_TSO500S_Data]"
    - "[TSO500HRD_Data]"
    - "[Cloud_TSO500HRD_Data]"

jointFiles:
  purityPloidyFiles: Logs_Intermediates/CombinedVariantOutput/{pairId}/{pairId}_CombinedVariantOutput.tsv, Optional
  gisFile: Logs_Intermediates/Gis/{sampleId.DNA}/{sampleId.DNA}.gis.json, Optional
  msiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.microsat_output.json, Optional
  tmbFile: Logs_Intermediates/Tmb/{sampleId.DNA}/{sampleId.DNA}.tmb.metrics.csv, Optional
  lohFiles:
    - Logs_Intermediates/Gis/{sampleId.DNA}/{sampleId.DNA}.abcn_genes.tsv, Optional    
  snvFiles: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.hard-filtered.vcf.gz, Optional
  cnvFiles:
    - Logs_Intermediates/Gis/{sampleId.DNA}/{sampleId.DNA}.abcn_annotated.vcf, Optional
    - Logs_Intermediates/LrCalculator/{sampleId.DNA}/{sampleId.DNA}_DragenExonCNV.vcf, Optional
    - Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.cnv.vcf.gz, Optional
  rnaSpliceFiles: Logs_Intermediates/RnaSpliceVariantCalling/{sampleId.RNA}/{sampleId.RNA}_SpliceVariants.vcf, Optional
  rnaFusionFiles:
    - Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.fusion_candidates.vcf.gz, Optional
    - Logs_Intermediates/RnaFusion/{sampleId.RNA}/{sampleId.RNA}_AllFusions.csv, Optional
  rnaGeneExpressionFiles:
    - Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.quant.genes.sf, Optional
  metricsQCFile: Logs_Intermediates/MetricsOutput/MetricsOutput.tsv

sampleFiles:
  tumorPairId:
    visualizationFiles:
      coverageFiles-additional-v55:
        - Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.tn.bw, Optional
        - Logs_Intermediates/Gis/{sampleId.DNA}/{sampleId.DNA}_logRatio.tsv, Optional
      coverageFiles:
        - Logs_Intermediates/DnaDragenExonCnvCaller/{sampleId.DNA}/{sampleId.DNA}.target.counts.gc-corrected.gz, Optional
      coverageBedFiles:
        - "Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.target_bed_read_cov_report.bed, Optional"
      ballelesFiles: Logs_Intermediates/Gis/{sampleId.DNA}/{sampleId.DNA}.baf.bedgraph.gz, Optional
    alignmentFiles:
      dnaBamFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.bam, Optional
      dnaBaiFile: Logs_Intermediates/DnaDragenCaller/{sampleId.DNA}/{sampleId.DNA}.bam.bai, Optional
      rnaBamFile: Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.bam, Optional
      rnaBaiFile: Logs_Intermediates/RnaDragenCaller/{sampleId.RNA}/{sampleId.RNA}.bam.bai, Optional
```


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