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Mutation rate in AlphaPeel #164

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XingerTang opened this issue May 22, 2024 · 3 comments
Open

Mutation rate in AlphaPeel #164

XingerTang opened this issue May 22, 2024 · 3 comments
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enhancement New feature or request

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@XingerTang
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@gregorgorjanc
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We should clarify what mutation rate is used in AlphaPeel and we should possibly make it as an input parameter (assuming we do not have this yet!?)

@gregorgorjanc gregorgorjanc added the enhancement New feature or request label May 22, 2024
@AprilYUZhang
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Does this mean rewriting an existing penetrance function？

@gregorgorjanc
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Last time I checked I think that mutation rate is baked (fixed) in the code - in the Mendelian transmission function. The penetrance function deals with genotyping and sequencing errors. While we provide a way to specify these error rates, we do not provide a way to specify mutation rate (I think).

@AprilYUZhang please check this and let’s work on this aspect via this issue. Thanks!

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@gregorgorjanc @XingerTang @AprilYUZhang