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Encoding of genotypes is confusing and error prone #175

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kbroman opened this issue Sep 17, 2020 · 0 comments
Open

Encoding of genotypes is confusing and error prone #175

kbroman opened this issue Sep 17, 2020 · 0 comments
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@kbroman
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kbroman commented Sep 17, 2020

As I understand what I've done, genotypes in 2-way RIL should be coded as 1 or 2.

But for multi-parent populations, I'm assuming SNPs coded 1/2/3, and so inbred founders should have codes 1 and 3, and then offspring lines (4-way RIL, 8-way RIL, etc) should similarly be coded 1 and 3. If someone uses the codes 1 and 2 in this case, is there a warning issued or are the results just messed up?
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