[User Story] Rebuild GENS PON for better X coverage

[mathiasbio]

Need

As a clinician I want to be able to detect copy-number variations in the X chromosome in XY individuals based on the way the current PON has been built the coverage is very sparse in the X chromosome for XY individuals. There are new instructions on Atlas using nfcore which has a new setting ""gens_min_interval_median_percentile": 5," which should be able fix this issue!

Suggested approach

If rebuilding the PON takes a lot of computational effort it might be worthwhile to wait for the new Watchmaker kit at which point the PON would need to be rebuilt regardless. So check that and make a decision!

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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