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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
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Should the copy number segments be filtered before COPY NUMBER MATRIX GENERATION? #182

Closed YingYa closed 4 months ago

YingYa commented 6 months ago

Hi,

I would like to run de novo extraction for copy number from a cancer cohort that contains both male and female. Should the copy number segments of chrX and chrY be filtered before COPY NUMBER MATRIX GENERATION? I have tried to find the processing details on the paper "Signatures of copy number alterations in human cancer", but got little.

azhark2 commented 4 months ago

Hi,

The copy number matrix generation occurs downstream of the copy number calling itself. Whether chrX and chrY should be filtered depends on the biological question and is at the users discretion, and must be done at the copy number calling step, prior to matrix generation.