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Defining tumor purity/ploidy #414

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mbenary opened this issue Jul 11, 2023 · 0 comments · Fixed by #453
Closed

Defining tumor purity/ploidy #414

mbenary opened this issue Jul 11, 2023 · 0 comments · Fixed by #453
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enhancement New feature or request

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@mbenary
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mbenary commented Jul 11, 2023

Is your feature request related to a problem? Please describe.
Tumor purity is important to have context for variant allele frequencies. The available wrapper for ascat is not in a stable state and output is not available for cbioportal-export.

Describe the solution you'd like
First, the wrapper for ascat needs to be tested. Second, the output needs to be available for cbioportal-export and that should be homogenous across different tools.

Describe alternatives you've considered
Other options for tools would be Theta2 or PureCN. Maybe a comparison of tools to understand robustness is necessary.

Additional context
None.

@mbenary mbenary added the enhancement New feature or request label Jul 11, 2023
@ericblanc20 ericblanc20 linked a pull request Oct 11, 2023 that will close this issue
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