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AlexandrovLab / SigProfilerSingleSample

SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability for each signature to cause a specific mutation type in the sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
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Can ID signatures be run on vcfs from build 38? #21

Closed bzhang19 closed 1 year ago

bzhang19 commented 1 year ago

Hello! Looking at the COSMIC website, the ID signatures are all derived from build 37. Is it possible to extract COSMIC ID signatures from build 38 vcfs? Thanks for your time!

marcos-diazg commented 1 year ago

Hi @bzhang19,

Thanks for reaching out. As explained in the COSMIC Mutational Signatures downloads website (https://cancer.sanger.ac.uk/signatures/downloads/), there is no renormalization available for the reference ID signatures, in contrast to SBS and DBS signatures. However, you can always extract de novo ID signatures from your GRCh38-aligned genomic data using SigProfilerExtractor.

I'll proceed to close this ticket as it's not related to our legacy SigProfilerSingleSample package, but happy to follow up over email (mdiazgay@health.ucsd.edu) if you have further questions.