Virus Interpreter is a VIRUSBreakend post-process algo that takes in the final VIRUSBreakend summary and adds annotation and interpretation and performs filtering for reporting. The algo writes a "virus.annotated.tsv" where every line is an annotated viral presence from the VIRUSBreakend summary file.
Virus Interpreter picks the reference taxid that should be displayed in a report and performs a look-up in the taxonomy db to find the matching virus name.
Virus Interpreter allows the mapping of any species taxid to either "HPV", "EBV" ,"MCV", "HBV" or "HHV-8". Within the Hartwig pipeline this configuration is used to map all clinically relevant HPV species to "HPV" which in turn is used to label patients as "HPV positive" or "HPV negative".
Every virus found by VIRUSBreakend is evaluated for reporting. For a virus to be reported, the following conditions need to be met:
- The virus should be present in the whitelist
- VIRUSBreakend must have found at least 1 integration site into the tumor DNA for "HPV", "MCV", "HBV" or "HHV-8"
- For "EBV" next to the at least 1 integration site the following conditions should extend with:
- Coverage of the virus should be greater than 90%
- Mean depth of virus should be greater than the expected clonal depth
- For "EBV" next to the at least 1 integration site the following conditions should extend with:
- VIRUSBreakend has none integration sites into the tumor DNA for "HPV", "MCV", "HBV", "EBV" or "HHV-8" and the conditions should extend with:
- Coverage of the virus should be greater than 90%
- Mean depth of virus should be greater than the expected clonal depth
- The VIRUSBreakend QC status must not be
LOW_VIRAL_COVERAGE - The virus must not be blacklisted.
The blacklist is configurable and used in the Hartwig pipeline to filter any forms of HIV from getting reported. The whitelist is configurable and used in the Hartwig pipeline to filter which virus we want to report.
Virus Interpreter produces a tsv file where every line (record) is an entry from the VIRUSBreakend summary file. The following fields are stored per viral presence:
| Field | Description |
|---|---|
| taxid | The reference taxid of the virus that is called with VIRUSBreakend |
| name | The name of the virus, matching with the taxid |
| qcStatus | The QC status as reported by VIRUSBreakend |
| integrations | The number of detected integrations of this virus into the sample genome as reported by VIRUSBreakend |
| interpretation | The output of the interpretation step of Virus Interpreter |
| percentageCovered | The percentage of the viral reference sequence that has been covered in the tumor sample as reported by VIRUSBreakend |
| meanCoverage | The mean coverage of the virus as reported by VIRUSBreakend //TODO: improve |
| expectedClonalMeanCoverage | The expected coverage assuming the virus is clonally integrated once in the tumor DNA |
| reported | A boolean indicating whether the detected viral presence is considered a driver |
- [1.1] (coming)
- New reporting strategy of viruses to report only clinical relevant viruses
- 1.0
- Initial release.