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morrislab / phylowgs

Application for inferring subclonal composition and evolution from whole-genome sequencing data.
GNU General Public License v3.0
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Automating tree extraction and plotting #109

Closed underbais closed 5 years ago

underbais commented 5 years ago

Hello devs,

I wonder if you would have any comments/thoughts on a possible python pipeline for automated best tree (a first few) extraction and plotting along with CCF info. I mean js/browser implementation is great but not really automation-friendly.

Any advise?

Thanks!

aleighbrown commented 5 years ago

For what's it worth, if you check out the snakemake pipeline for PWGs that I have, I've got a pretty scrappy script that sort of does this....the whole thing was written for the NIH biowulf cluster as well, so you might be able to adapt it to your needs. https://github.com/aleighgreen/pwgs_snakemake/blob/master/parse_pwgs_output.py

underbais commented 5 years ago

Awesome, thank you for sharing! I kind of did the same in R but will definitely check this out