[User Story] Rebuild PONs with new samples and bioinfo-methods

[mathiasbio]

Need

As a clinician I want noiseless coverage profiles and accurate CNV calls. We have PONs for 3 panels built, but the samples used in their construction have been sequenced or prepped or analysed bioinformatically with methods with carry their own inherent coverage-biases and which may not be consistent with the biases existing in the current production workflow. This means that the PONs may not be working optimally, as has been raised in ticket: https://clinical-scilifelab.supportsystem.com/scp/tickets.php?id=69121

Beyond these updates we are also currently underway with a new update to the TGA workflow, where UMIs will be used to remove duplicates, which may most likely also affect the coverage profiles in some ways. Probably here we would be forced to rebuild the PONs anyway, and it would be a good opportunity to get more recent samples that also reflect the new lab methods.

Suggested approach

Collect recent samples for existing panels and rerun about 50 - 100 for each panel (mixed sexes) with the updated UMI collapsed TGA workflow.

Considered alternatives

No response

Deviation

No response

System requirements assessed

• Yes, I have reviewed the system requirements

Requirements affected by this story

No response

Risk assessment needed

• Needed
• Not needed

Risk assessment

No response

SOUPs

No response

Can be closed when

No response

Blockers

No response

Anything else?

No response