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AlexandrovLab / SigProfilerMatrixGenerator

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
BSD 2-Clause "Simplified" License
100 stars 37 forks source link

exome=True label #120

Closed britneyting closed 1 year ago

britneyting commented 1 year ago

Hi, the documentation for the "exome" flag states that if "exome=True", the matrix generator will "Downsample mutational matrices to the exome regions of the genome". If we are already using exome data, should we set this flag to True or False? I tried both and used SigProfilerExtractor, and it seems like the different signatures are extracted for each case, so not sure which flag to use.

mdbarnesUCSD commented 1 year ago

Hi @britneyting,

You will want to set exome=True for running SigProfilerExtractor with exome data.

Thanks!