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Refining tumor/normal assignment #209

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nandobonf opened this issue Oct 29, 2024 · 0 comments
Open

Refining tumor/normal assignment #209

nandobonf opened this issue Oct 29, 2024 · 0 comments

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@nandobonf
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nandobonf commented Oct 29, 2024

Dear authors,
I successfully ran Numbat on multiple samples, however in some cases I would need to refine the tumor/normal definition (or eventually remove "noisy" CNV calls such as the BAMP). In the case shown below, for example, it is clear that genotypes 1 and 2 demote normal cells, instead, Numbat only calls genotype 1 as "normal". You can see the Numbat tumor/normal annotation labeled as "type" in the heatmap below.
Any suggestions would be highly appreciated.
Thanks in advance.

image
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