support MAF files?

[wangzunq]

Hi, I finished SIgProfilerAssignment and got matrices in the output. Which matrices should I use as input to SigProfilerExtractor? I see it doesn't support MAF files for each samples like SigProfilerAssignment and SigProfilerMatrixGenerator. Please correct me if I misunderstand something or what should be the correct approach?

[mdbarnesUCSD]

Hi @wangzunq,

SigProfilerAssignment is a tool for assigning mutational signatures and SigProfilerExtractor does de novo signature extraction. The input for both tools is a mutational counts matrix, which can be generated using SigProfilerMatrixGenerator.

If you have the counts matrix, you can run with matrix as input and set the parameter input_type=matrix. Otherwise, if your inputs are MAF set input_type=vcf.

[wangzunq]

Thank you for explanation. I got matrices from SigProfilerMatrixGenerator, there are several under SBS folder. Should I use this folder as input to do extractor? Currently focus on SBS only.

Zunqiu Wang

Computational Biologist I

CLL Center, J. Brown lab

Dana Farber Cancer Institute | Department of Medical Oncology

450 Brookline Ave

SM 648

Boston, MA 02215

https://brownlab.dana-farber.org/

On Aug 27, 2024, at 12:38, mdbarnesUCSD @.***> wrote:



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Hi @wangzunqhttps://github.com/wangzunq,

SigProfilerAssignment is a tool for assigning mutational signatures and SigProfilerExtractor does de novo signature extraction. The input for both tools is a mutational counts matrix, which can be generated using SigProfilerMatrixGeneratorhttps://github.com/alexandrovlab/SigProfilerMatrixGenerator.

If you have the counts matrix, you can run with matrix as input and set the parameter input_type=matrix. Otherwise, if your inputs are MAF set input_type=vcf.

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[mdbarnesUCSD]

Yes, you will provide the path to one of those input matrices. You can learn more about these contexts on the wiki page for SigProfilerMatrixGenerator and in more detail in the publication.

Please reach out if you have any additional questions.