[User Story] Delivery of additional CNV and BAF files to Caesar

[mathiasbio]

Need

As a researcher / clinician doing interpretation of CNVs from tumor normal matched WGS analyses I would like to have access to:

• the BAF plots loaded into GENS but in a format accessible by IGV (because when working from home GENS can be too slow)
• the CNV.somatic.*.ascat.copynumber.txt.gz file but from the normal sample which can be useful to get the uniparental disomy

See freshdesk ticket with request: https://scilifelab.freshdesk.com/a/tickets/1000758

Suggested approach

For Ascat: I don't know if Ascat produces this file from the normal sample, and I can't see if it is because all outputs from Ascat are saved in a temporary folder which is deleted on completion.

• Verify that Ascat produces the file for the normal sample
• If above is true then we just need to save this and store + deliver it

For BAF tracks in IGV::
Maybe we can expand the functionality of the GENS script to have an IGV option where the BAF folder does not have the GENS specific zoom levels. Then we can just add an additional rule, baf_to_igv or something, and use this script, then store an deliver.

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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