Question: Mutation Burden file and manual curation
0
gravatar for twtoal
5 months ago by
twtoal0
twtoal0 wrote:

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

 

ADD COMMENTlink modified 5 months ago • written 5 months ago by twtoal0
Answer: Mutation Burden file and manual curation
0
gravatar for markus.riester
5 months ago by
markus.riester110 wrote:

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. 

ADD COMMENTlink written 5 months ago by markus.riester110
Answer: Mutation Burden file and manual curation
0
gravatar for twtoal
5 months ago by
twtoal0
twtoal0 wrote:

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.

 

ADD COMMENTlink written 5 months ago by twtoal0
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