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.

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Last updated 5 months ago

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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.