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odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool
MIT License
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missing genotypes in scaffold #40

Closed 23andme-jaredo closed 3 years ago

23andme-jaredo commented 3 years ago

Are missing genotypes allowed in the scaffolds?

For example:

0|1 ./.
./. 0|1

The use case is samples coming from different microarrays.

thanks!

Jared

odelaneau commented 3 years ago

Hey Jared,

I hope you're okay!

S4 only considers genotypes in the scaffold (--scaffold) that are: (i) phased (i.e. "|"), (ii) heterozygous, (iii) consistent with input data (--input).

All genotypes that do not pass (i) to (iii) are simply ignored. It doesn't matter if the scaffold retained from one sample to the other massively differs.

Best

23andme-jaredo commented 3 years ago

That's great. Thanks.