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Add MSI measure #413

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mbenary opened this issue Jul 11, 2023 · 0 comments · Fixed by #427
Closed

Add MSI measure #413

mbenary opened this issue Jul 11, 2023 · 0 comments · Fixed by #427
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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.
MSI status is a relevant feature to describe tumor stability and is relevant for clinical decision-making. Currently, snappy provides MANTIS, but there are other options available.

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

Describe alternatives you've considered
Provide wrapper for other MSI callers, which allow tumor-only samples, such as MSIsensor2 which is used by TCGA

Additional context
None.

@mbenary mbenary added the enhancement New feature or request label Jul 11, 2023
@giacuong171 giacuong171 linked a pull request Aug 7, 2023 that will close this issue
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