[QUESTION] Partially phased VCF as input

[davidyuyuan]

(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?

[Maarten-vd-Sande]

I am also wondering about this.

Taking the liberty to tag @odelaneau

[krferrier]

Based on this thread: #57 , it appears that Shapeit5 does not consider partially phased variants. It will phase all variants regardless of whether they were previously phased or not. Shapeit4 does have this capability though and there is discussion on how to utilize Shapeit4 and 5 to leverage the partial phasing output by read-based methods (whatshap) with Shapeit4 and the improved rare-variant phasing of Shapeit5.