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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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Manta VCFs #48

Closed alexanderchang1 closed 2 months ago

alexanderchang1 commented 8 months ago

Hi,

Does anyone in the lab have any experience trying this for Manta-called SVs? My project is specifically focusing on large structural variations.

Thank you!

ethanumn commented 6 months ago

Sorry for the slow response -- I'm not aware of anyone who has applied Pairtree on structural variants. If you are able to successfully use Pairtree for this use case please let us know!

alexanderchang1 commented 6 months ago

Hi,

I was unable to, as Manta VCF files don't convert cleanly to the necessary input required for pairtree. I do have a second question though, I work in a translational setting where many primary tumors are FFPE from the clinical archives. Have you guys done benchmarking of pairtree in terms of robustness in relation to FFPE artifacts?

Thank you!

ethanumn commented 6 months ago

I do not believe we've done any benchmarking of Pairtree related to FFPE artifacts.