# 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                                                                                                                                                                                                                 |
| -------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| <p>- Sample ID<br>- Output date<br>- Output time<br>- Pipeline version (Docker image version number)</p> | <p>- Run name<br>- Run date<br>- Sample index ID<br>- Instrument ID<br>- Instrument control software version<br>- Instrument type<br>- RTA version<br>- SBS reagent cartridge lot number<br>- Cluster reagent cartridge lot number</p> |

## 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 fusion filtering criteria with "PASS" from DNAFF module
  * 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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