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Roth-Lab / pyclone-vi

Fast method for inferring cancer clonal population structure from SNV data.
GNU General Public License v3.0
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Pre-processing query #27

Open seedgeorge opened 1 year ago

seedgeorge commented 1 year ago

Hi, I have multi-sample mutation data (mutect2) and also copy number data (battenberg). I'm happy creating the input files with allele counts, but was wondering about best practices for battenberg, as it reports both clonal and sub-clonal entries for CNAs? Kind regards, George

aroth85 commented 1 year ago

Best bet it to use the clonal CNA calls. In principle these should be more common and account for more of the signal.

seedgeorge commented 1 year ago

Great, thanks. So I'll exclude mutations that overlap with areas of sub-clonal CNAs. In the future it'd be nice to model them in a more integrative manner...