[User Story] Integrate TGA CNV results into GENS

[mathiasbio]

Need

As a hospital geneticist diagnosing patients from TGA data I want to be able to detect common CNVs on as small a scale as possible. Currently CNVs are uploaded to Scout in two formats, as variants in a VCF, and as visual plots in a PDF-report (with LoH information in a table). Typically however, correctly interpreting CNVs requires looking at coverage data and VAF - info manually, which is not possible to do now except perhaps through some tedious work in IGV.

It would be good if CNVs from TGA samples could be visualised in GENS similar to what is done for WGS.

This may be a solution that could satisfy the feedback here: #1366

Suggested approach

Format CNVkit results to GENS:

• Apparently Lund is doing this already, based on results from CNVkit -- which is formatted in some way to make it work in GENS.
• We should investigate if we can do the same.
• Then request feedback from customers (which customers?)
• Make necessary adjustments from feedback / Open new issues with feedback if it is outside the scope
• Implement in Balsamic

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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