[QUESTION] Partially phased VCF as input

odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool

https://odelaneau.github.io/shapeit5/

MIT License

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[QUESTION] Partially phased VCF as input #106

Open davidyuyuan opened 1 month ago

davidyuyuan commented 1 month ago

(I was unable to find an answer by reading the documentation.)

If an input VCF is partially phased, would Shapeit5 apply its phasing logic to all variants regardless they are phased or not? Or, it would only try to phase the variants yet to be phased?