Opened 3 days ago

Last modified 3 days ago

#1624 new task

Mutational signatures

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v5.5
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

See ​https://cancer.sanger.ac.uk/signatures/

We should implement the different signature that are described here:

  • For WGS variant calling: SBS, DBS and ID
  • For WGS structural variant calls: SV
  • For Copy number: CN
  • For RNAseq: RNA SBS

We already have the SBS signature implemented as part of the WGS variant calling pipeline (but there seems to be a bug so the results should not be trusted!).

We should get rid of the current implementation and instead create a new step in the pipelines that create new child items to the variant call items (for example MutationalSignature). For each pipeline the relevant data files and a plot for the signatures should be created.

Change History (2)

comment:1 by Nicklas Nordborg, 3 days ago

Description: modified (diff)

comment:2 by Nicklas Nordborg, 3 days ago

In 7933:

References #1624: Mutational signatures

Created MutationalSignature subtype and related annotation type categories for WGS.

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