Mutation Burden file and manual curation
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twtoal • 0
@twtoal-15473
Last seen 6 months ago

Is the mutation burden file produced by Dx.R affected at all by the purity/ploidy selection in the manual curation .csv file?

 

purecn mutation_burden manual_curation • 283 views
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@markusriester-9875
Last seen 28 days ago

It affects the posterior probabilities of the germline vs somatic classification, but these are fairly robust to errors in purity and ploidy. So if you don't see a difference, that's not unexpected. 

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twtoal • 0
@twtoal-15473
Last seen 6 months ago

Okay, I'm just working on some reorganization to my pipeline.  I've decided to duplicate all the PureCN.R output files, one set prior to manual curation and the second after it.  I think I'll run Dx.R on the manually curated output, no need to run it on the initial output.

 

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