Mutational signatures

[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.

[Nicklas Nordborg]

In 7933:

References #1624: Mutational signatures

Created MutationalSignature subtype and related annotation type categories for WGS.

[Nicklas Nordborg]

In 7934:

References #1624: Mutational signatures

Started to implement the "Start mutational signatures" wizard. There are three entry points: Simple variants, structural variants and copy number.

[Nicklas Nordborg]

In 7935:

References #1624: Mutational signatures

Added a container definition with the COSMIC SigProfiler software that is needed for generating signatures.

[Nicklas Nordborg]

In 7936:

References #1624: Mutational signatures

Implemented the first part of the analysis. Jobs can be submitted to the cluster and the signature counts files and plots are created. It has been tested with simple variants calls from the WGS pipeline and copy number segment information.

[Nicklas Nordborg]

In 7937:

References #1624: Mutational signatures

Removed SBS96 from the WGS variant calling script.

[Nicklas Nordborg]

In 7938:

References #1624: Mutational signatures

WGS variant calls are now added to the mutational signatures pipeline when the are manually confirmed. The auto-confirm wizard should also start the analysis.

[Nicklas Nordborg]

In 7939:

References #1624: Mutational signatures

SBS96 removed from the Case summary and release export.

[Nicklas Nordborg]

In 7940:

References #1624: Mutational signatures

Updated the thumbnails extensions to the new signature plots.

[Nicklas Nordborg]

In 7941:

References #1624: Mutational signatures

Ascat results are now added to the mutational signatures pipeline when they are accepted.

[Nicklas Nordborg]

In 7942:

References #1624: Mutational signatures

Mutation signatures from structural variants should now work. Assuming that a 'breakpoints.bedpe' exists on the variant call item (not yet implemented) we can relatively easy fix that file so that it works with COSMIC. The fixes are:

1. We need to add a header line
2. We need to add an "sample" column as the first colum

[Nicklas Nordborg]

In 7943:

References #1624: Mutational signatures

Also save the "SV32.annotated.tsv". It contains information about how the variants have been classified which could be useful information.

[Nicklas Nordborg]

In 7945:

References #1624: Mutational signatures

Updated the thumbnails extensions to the display signatures for the structural variants.

[Nicklas Nordborg]

In 7947:

References #1624: Mutational signatures

Started to implement support for the RNAseq variant calls in the mutational signatures pipeline.

[Nicklas Nordborg]

In 7948:

References #1624: Mutational signatures

It should now work with the RNAseq pipeline as well.

[Nicklas Nordborg]

In 7949:

References #1624: Mutational signatures

Removing mutational signatures code that is part of the RNAseq variant call step.

[Nicklas Nordborg]

In 7950:

References #1624: Mutational signatures

The manual confirmation wizard for RNAseq variant calls now add items to the mutational signatures pipeline if it found at least one variant. The auto-confirm wizard has also been updated to start the mutational signatures pipeline.

[Nicklas Nordborg]

In 7956:

References #1624: Mutational signatures

Updated the thumbnails extensions to the display signatures for INDEL mutations (ID83).

[Nicklas Nordborg]

In 7957:

References #1624: Mutational signatures

Added a step for running SigProfilerAssignment for SBS96, DBS78, ID83, SV32 and CNV48 (but no results are saved yet).

[Nicklas Nordborg]

In 7958:

References #1624: Mutational signatures

Switch place of "normal alignment name" and mutation count in the pdf plot, but only if a normal alignment name has been specified.

[Nicklas Nordborg]

In 7959:

References #1624: Mutational signatures

Save 3 output files from the SigProfilerAssignment output.

• Assignment_Solution_Activities.txt which contains the number of variants assigned to each signature
• Assignment_Solution_Samples_Stats.txt
• Assignment_Solution_Signature_Assignment_log.txt

[Nicklas Nordborg]

In 7963:

References #1624: Mutational signatures

Adding annotation types for mutational signatures.

[Nicklas Nordborg]

In 7964:

References #1624: Mutational signatures

Also save the Decomposed_MutationType_Probabilities.txt file and do not generate any plots.

[Nicklas Nordborg]

In 7969:

References #1624: Mutational signatures

Remove a stray space from signature names.

[Nicklas Nordborg]

In 7970:

References #1624: Mutational signatures

Importing signature mutation counts to annotations.

[Nicklas Nordborg]

In 7977:

References #1624: Mutational signatures

Remove scripts that are no longer used.

[Nicklas Nordborg]

In 7978:

References #1624: Mutational signatures

Implemented auto-confirm for mutational signatures. The results are accepted if the job didn't fail, otherwise the items are deleted and the parent item is re-scheduled for another try.