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raphael-group / THetA

Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This repository includes the updated algorithm, called THetA2.
http://compbio.cs.brown.edu/projects/theta/
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BAF? #6

Closed SooLee closed 8 years ago

SooLee commented 8 years ago

Hello,

Thanks for the program. Just a quick question. Does THetA 0.6 take BAF as input? I might be missing it from MANUAL.txt - the input format doesn't seem to contain BAF information. (I got an impression from the paper that THetA2 uses BAF as well as read depths.) Thanks in advance!

S.

gsatas commented 8 years ago

Hello, thanks for your interest in THetA. The current release of THetA doesn't take BAFs as input, but we provide a post-processing script that uses BAF to choose between multiple THetA solutions. This script is runBAFGaussianModel and is described in the manual in section 9. We are also working on a version that will take BAFs directly as input and this will be released in the coming weeks.

SooLee commented 8 years ago

Thanks for your answer. My MANUAL doesn't have section 9, though. Is it a part of the current release?

SooLee commented 8 years ago

Would you be willing to release another version based on the current codes? It seems that have been many updates since the latest release and I see that section 9 is among those updates. Thanks.

gsatas commented 8 years ago

It looks like version 0.62 includes the BAF code, which is currently in the repository. As mentioned, we're in the process of putting together a new major release, which will be available soon.

SooLee commented 8 years ago

Ok, thanks.