"Clustered Trees" View is empty and inferring sequence of mutations

[zafarali]

Hi,

(1) My "clustered trees" view is empty. What am I supposed to see in this panel? (2) In your paper, Fig 4 and Fig 10 shows some inferred trees with the mutations superimposed. All I have is the number of SSMs assigned to each cluster. I was wondering where I can get the assignment of each SSM to the cluster? Am I supposed to calculate the CCF myself and assign it accordingly?

Thanks!

[BhaktiDwivedi]

Hi,

I was wondering if you were able to obtain the above? I am also trying to get information similar information; however, I am not sure how to interpret/derive the data from the results in this context.

Briefly, I generated the 'ssm_data.txt' from a vcf file for genes of interest. I would like to run the program without any CNVs, hence I provide an empty 'cnv_data.text' file.

I was able to successfully run PhyloWGS under default settings and test_results files were generated from the run.

I am having difficulty in interpreting these results. I was hoping to see Figures similar to Figure. 9 and Figure. 10 of the paper (http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0602-8). Could you please help me understand how can I obtain such figures from my current result files?

To clarify, for instance, I have 7 gene mutations in 8 different tumor samples, I want to see how many sub-populations exist within my samples. Essentially, what samples are grouped in what sub-population, in how many sub-populations/lineage and what percentage (if any) given the somatic mutations data, and what ssm support that specific sub-population.

I would greatly appreciate any help and suggestions. Thank you!

[zafarali]

Hi!

From what I understood from your question, this might help you:

So I ran my PhyloWGS run like this:

python ./phylowgs-smchet5/evolve.py ssm.txt cnv_empty.txt
python ./phylowgs-smchet5/write_results.py ./ ./trees.zip summ.json.gz muts.json.gz mutass.zip --include-ssm-names

If you take a look at top_k_trees file it gives you a tree and the assignment of genes to each node.

Let me know if this helps!

[BhaktiDwivedi]

Thank you. This helps but I was wondering how to also obtain inferred subpopulation composition break down by each sample? something like Figure 10 of PhyloWGS paper.

[BhaktiDwivedi]

I meant Figure 9 not Figure 10, i.e., the sub clonal composition inference for each tumor sample.