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AlexandrovLab / SigProfilerAssignment

Assignment of known mutational signatures to individual samples and individual somatic mutations
BSD 2-Clause "Simplified" License
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Unclear Scope #134

Closed DarioS closed 2 months ago

DarioS commented 3 months ago

README file doesn't explain difference to SigProfilerSingleSample. Also, it seems SigProfilerAssignment can't do structural variants.

mdbarnesUCSD commented 3 months ago

Hi @DarioS,

SigProfilerAssignment does support structural variants through matrix inputs but you are correct that it does not process structural variants via bedpe inputs. If you do not have a matrix though, then as of SigProfilerAssignment v0.1.7 you will need bedpe files that adhere to this format specified in SigProfilerMatrixGenerator.

We will look to add support for this in the next release.

DarioS commented 3 months ago

I don't think it can work with any kind of input. There seems to be no suitable value of context_type that a user could specify.

context_type: String. Valid options include "96", "288", "1536", "DINUC", and "ID".

In addition, the web server version has no radio button option for S.V.

image

Finally, there is no mention of structural variant support in README file.

mdbarnesUCSD commented 3 months ago

The context_type parameter is not relevant for matrix input. The most current version of code is what is hosted in this repository. We will expand the documentation on the README to help make things more clear.

rvangara commented 2 months ago

Hi @DarioS,

To answer your question regarding SigProfilerSingleSample: it is an older version of the assignment tool and is no longer under development. We might archive it soon. All further developments will be done on the SigProfilerAssignment tool.

DarioS commented 2 months ago

I shall focus on using SigProfilerAssignment.