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morrislab / pairtree

Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneity. Pairtree focuses on scaling to many more cancer samples and cancer cell subpopulations than other algorithms, and on producing concise and informative interactive characterizations of posterior uncertainty.
MIT License
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var_read_prob column in the .ssm file #31

Closed pushpa-itagi closed 1 year ago

pushpa-itagi commented 2 years ago

Hi,

I am intending to use pairtree to generate clonal evolution tress for bladder cancer samples in multiple patients. I am confused about the var_read_prob values that are needed, which indicate the CNA correction. 1) is this probability the same as multiplicity of a mutation ? (Peter Van Loo 2021 sub-clonal reconstruction, Nature methods)? 2) Is it a probability which depends on major and minor copy numbers? So, Major CNA(Major CNA + Minor CNA).

Can you please share more information on this ? the .ssm in example folder seems to come from a diploid genome, and a lot of mutations in my dataset are not having a diploid locus.

Thanks

Regards, Pushpa Itagi

ethanumn commented 2 years ago

Hi Pushpa --

I'd be glad to answer your questions.

  1. It's closely related see here: https://github.com/morrislab/pairtree/issues/17
  2. Yes, it is. The issue I linked to in (1) provides more detail.

Our newly released protocol paper provides further examples and explanations about the .ssm file that go beyond what's provided in the Pairtree repository readme. Please see here: https://pubmed.ncbi.nlm.nih.gov/36129821/

What might be particularly helpful in this paper is the "Before you begin" section related to Pairtree inputs.

Please let me know if you have any more questions. Ethan