Dear Developers,
Thank you very much for developing and maintaining SigProfilerTopography. We greatly appreciate the effort that has gone into this tool.
While testing SigProfilerTopography, we encountered two questions and would appreciate your guidance:
(1) Availability of probability matrix files for cancer types other than BRCA
In the example data (21BRCA), the provided probability matrix files (e.g. 21BRCA_probabilities) are based on BRCA and include probability matrices for single base substitutions (SBS) and doublet base substitutions (DBS).
We are particularly interested in other cancer types like endometrial cancer, and we were wondering:
Are probability matrix files available for cancer types other than BRCA? If so, where can these files be obtained? If not, is the recommended approach to generate these probability matrices ourselves from WGS data? Any guidance on the standard workflow for non-BRCA cancer types would be very helpful.
(2) SigProfilerTopography hanging when INDELs are included in the input matrix
When running the example code, we observed the following behavior:
If the input matrix contains only single base substitutions (SBS), SigProfilerTopography runs successfully.
However, when the input matrix also includes small insertions and deletions (INDELs) (for example, mutations such as A → ATTATT), the pipeline appears to stall at the step “SigProfilerAssignment for INDELs using COSMIC fit”, and does not proceed to subsequent steps.
We would like to ask:
Is this a known issue when running SigProfilerTopography with INDELs? Are there specific requirements or recommended settings for running INDEL analyses? Or does this indicate that INDEL-based analyses are more computationally demanding or less stable in the current implementation?
Thank you very much for your time and support. We look forward to your advice.
Best wishes,
Dear Developers,
Thank you very much for developing and maintaining SigProfilerTopography. We greatly appreciate the effort that has gone into this tool.
While testing SigProfilerTopography, we encountered two questions and would appreciate your guidance:
(1) Availability of probability matrix files for cancer types other than BRCA
In the example data (21BRCA), the provided probability matrix files (e.g. 21BRCA_probabilities) are based on BRCA and include probability matrices for single base substitutions (SBS) and doublet base substitutions (DBS).
We are particularly interested in other cancer types like endometrial cancer, and we were wondering:
Are probability matrix files available for cancer types other than BRCA? If so, where can these files be obtained? If not, is the recommended approach to generate these probability matrices ourselves from WGS data? Any guidance on the standard workflow for non-BRCA cancer types would be very helpful.
(2) SigProfilerTopography hanging when INDELs are included in the input matrix
When running the example code, we observed the following behavior:
If the input matrix contains only single base substitutions (SBS), SigProfilerTopography runs successfully.
However, when the input matrix also includes small insertions and deletions (INDELs) (for example, mutations such as A → ATTATT), the pipeline appears to stall at the step “SigProfilerAssignment for INDELs using COSMIC fit”, and does not proceed to subsequent steps.
We would like to ask:
Is this a known issue when running SigProfilerTopography with INDELs? Are there specific requirements or recommended settings for running INDEL analyses? Or does this indicate that INDEL-based analyses are more computationally demanding or less stable in the current implementation?
Thank you very much for your time and support. We look forward to your advice.
Best wishes,