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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
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Ped File #64

Closed AndrewSkelton closed 8 years ago

AndrewSkelton commented 8 years ago

Hi,

Would it be possible to add a flag, or functionality so the Ped file's Phenotype column could be interpreted as 0/1/-9 instead of the 1/2/0/-9 notation?

Thanks!

moonso commented 8 years ago

Guess so, do you mean:

0=unaffected
1=affected
-9=unknown

?

AndrewSkelton commented 8 years ago

Yep, that's exactly what I mean

moonso commented 8 years ago

Hi again,

after some consideration i'm not sure if this is a good idea. We have a standardised ped format, why would you leave that and add potential misunderstandings?

Måns

AndrewSkelton commented 8 years ago

In hindsight you're probably right, and feel free to close the issue. I generally adopted the 0 and 1 approach because it seemed more logical to me, but if the standard is 2 (affected), and 1 (unaffected), then there's no need to add another standard (https://xkcd.com/927/)

moonso commented 8 years ago

Haha Yes