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sigven / pcgr

Personal Cancer Genome Reporter (PCGR)
https://sigven.github.io/pcgr
MIT License
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Regional hypermutation (Kataegis) request #41

Closed hongiiv closed 4 years ago

hongiiv commented 6 years ago

Hi, Sigven, PCGR can analysis MSI and mutational signatures. Would you like to add Kataegis in the future?

You can see the Kataegis from mutalisk (http://mutalisk.org).

thanks!

sigven commented 6 years ago

Dear Changbum,

Great suggestion! I'd be happy to add functionality to indicate evidence of kataegis. Having looked at mutalisk.org, it seems the underlying software is not available for download(?), only available through the web, which makes it challenging for integration in PCGR. Correct me if i am wrong here.

If you are aware of similar tools (stand-alone packages available for download, i.e. R packages, Python programs etc.) intended for kataegis analysis, that would be great.

regards, Sigve

ohofmann commented 6 years ago

Sigve,

I tend to use SeqKat for this, although similar approaches are also present in other frameworks.

sigven commented 6 years ago

Thanks Oliver, this looks much more convenient! I'll start making a testbed for this asap.

Sigve

sigven commented 6 years ago

Would any of you (@ohofmann or @hongiiv) have a test case that shows evidence of kataegis?

ohofmann commented 6 years ago

I don't think I can share the sample that I have in mind but happy to run any (beta) versions you want me to explore and report back?

hongiiv commented 6 years ago

mutalisk have a demo vcfs for melanoma and lung cancer. You can check http://mutalisk.org/analyze.php

Benja1972 commented 5 years ago

Here my attempt to recreate it in Python https://github.com/Benja1972/bioinformatics/blob/master/Kataegis.py

sigven commented 4 years ago

Kataegis detection is now part of the workflow (when you include mutational signature analysis in your report , option --estimate_signatures)