Encoding GT for male on nonpar X

odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool

MIT License

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Encoding GT for male on nonpar X #24

Open mcieslik-mctp opened 4 years ago

mcieslik-mctp commented 4 years ago

How should genotypes (GT) for males be encoded in the NONPAR region as "0" "1" or "0/0" "1/1"?Both approaches seem to run. Thank you!

odelaneau commented 4 years ago

Hi,

It's a piece of work that remains to be done (i.e. haploid support). The behaviour of S4 on haploid genotypes is not tested at all. For now, I'd recommend making males as homozygotes on the X even though it's not ideal. I hope I'll soon find some time to properly do this :)

Best

mcieslik-mctp commented 4 years ago

Thank you for your answer, I guess this is the same as the recommendation for Beagle 5. Lot's of cool genes/variants on X - definitely worth supporting!