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raphael-group / decifer

DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).
BSD 3-Clause "New" or "Revised" License
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Generate state trees #6

Closed zlin77 closed 3 years ago

zlin77 commented 3 years ago

Dear developers,

Thank you for the contribution in addressing the question.

Currently when I run the codes on my samples, the report says for some mutations the given state tree file doesn't contain corresponding copy-number states, and when I tried to click the link to the manual to create all required state trees, the link was broken. Could you please provide a way to address this?

Best, Lin

simozacca commented 3 years ago

@brian-arnold has fixed the related documentation and provided a new functioning script for generating state trees specific to the input copy-number file. Please take a look at the new instructions at:

https://github.com/raphael-group/decifer#optionaldata

@brian-arnold please feel free to add any other important detail