zanmer / mesothelioma_evolution_deciphering_drugable_somatic_alterations Goto Github PK

Hello,

I notice that you did phylogenetic trees in CITUP with the output from PyClone.
However, In my work, run_analysis_pipeline commands can't give an output of mutations which didn't appear in all samples.
Which means, I can only make phylogenetic trees for the public mutations.

In your paper, I find you do make the cluster of private mutations, and also do citup.
How can you make that with no private mutations result from pyclone?

Below is my hypothesis:
You just classify each groups that are not public mutations as a specific cluster, and for the input file of run_citup_qip, you just use the formal mutations frequency data, and in the sample with no mutations, just put 0.

Thanks.

Dear Zanmer,

Thank you for sharing these scripts! I have one question about the clonal_analysis.R script.

The adjusted alt counts are calculated like this:
clonal_results$adjust_alt_counts = round(clonal_results$readcount * clonal_results$ccf.est/2)

where "clonal_results$readcount" is the total depth. Is this correct? Shouldn't that be "clonal_results$alt_count"?

Maybe I missed something. Thanks for your help!

Best wishes,
Lorinc

Hi,

I wanted to ask if you could explain a little how were the Copy number aberrations added as an input to REVOLVER? It will be great if I can get some more clarification on a method to follow to assign CCF and cluster to copy number changes.

Thanks