mathiasbio
commented
2 months ago I will run these samples on the updated version of Sentieon to make sure that we have the correct software-version specific artefacts present in the PON for the future, as we are intending to update Sentieon in the next release. https://github.com/Clinical-Genomics/BALSAMIC/issues/1384
Need
As a geneticst, despite not having a matching normal sample for germline filtering, I want to be sure that all somatic variants I am interpreting are true somatic variants, and not germline or artefacts.
To accurately filter out germline variants and artefacts from our true somatic calls, we could benefit from creating a TNscope PON. We already have LoqusDB germline calls from both our tumor-samples, and the rare-disease samples called in MIP as inhouse-databases for germline, and perhaps in that sense this TNscope PON may not contribute much in terms of filtering germline-variants, but may perhaps be most useful for filtering out common artefacts called by TNscope.
Suggested approach
Sentieon has some instructions here: https://support.sentieon.com/manual/TNscope_usage/tnscope/
Considered alternatives
No response
Deviation
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System requirements assessed
Requirements affected by this story
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Risk assessment needed
Risk assessment
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SOUPs
No response
Can be closed when
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Blockers
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Anything else?
No response