[User Story] Create TNscope PON

[mathiasbio]

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/

• Run TNscope according to above instructions on 100 male, and 100 female normal samples.
• Build the PON using the recommended bcftools command
• Test the PON on cases to understand the effects
• Implement in balsamic production if it seems useful

Considered alternatives

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Deviation

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System requirements assessed

• [ ] Yes, I have reviewed the system requirements

Requirements affected by this story

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Risk assessment needed

• [ ] Needed
• [ ] Not needed

Risk assessment

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SOUPs

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Can be closed when

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Blockers

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Anything else?

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