Combined Variant Output

File name: {SampleID}_CombinedVariantOutput.tsv

The combined variant file contains the variants and biomarkers in a single file. The output contains the following variant types and biomarkers:

• Small variants (including EGFR complex variants)

• Copy number variants

• Tumor Mutational Burden (TMB)

• MSI

• DNA Fusions

The combined variant output file also contains Analysis Details and Sequencing Run Details sections. The details of each are listed in the following table:

Analysis Details	Sequencing Run Details
- Sample ID - Output date - Output time - Pipeline version (Docker image version number)	- Run name - Run date - Sample index ID - Instrument ID - Instrument control software version - Instrument type - RTA version - SBS reagent cartridge lot number - Cluster reagent cartridge lot number

Variant Filtering Rules

Combined variant output produces small variants with blank fields in the following situations:

• The variant has been matched to a canonical RefSeq transcript on an overlapping gene not targeted by TruSight Oncology 500 ctDNA.

• The variant is located in a region designated iSNP, indel, or Flanking in the TST500_Manifest.bed file located in the Resources folder.

• Small Variants - All variants with the FILTER field marked as PASS and which have a canonical RefSeq transcript are present in the combined variant output.

  • Gene and transcript information is only present for variants belonging to canonical transcripts that are within the Gene list–Small Variants.

• Copy Number Variants - Copy number variants must meet the following conditions:

  • FILTER field marked as PASS.

  • ALT field is <DUP or <DEL> .

  • Gene is part of the copy number variant gene list

• Fusion Variants - Fusion variants must meet the following conditions:

  • Passing variant call (KeepFusion field is true).

  • Contains at least one gene on the fusion allow list.

  • Genes separated by a dash (-) indicate that the fusion directionality could be determined. Genes separated by a slash (/) indicate that the fusion directionality could not be determined.