Haplotype reference for ShapeIt (ShapeIt5)

Question

[evan.kransdorf]

Hello Biostar Friends,

Reaching out to those with experience doing phasing especially with ShapeIt (current version ShapeIt5).

Does anyone know what the best haplotype reference panel to use is? When you phase a small number of samples you need to use a reference. It seems like most are using 1000 genomes, but this itself looks like it was phased with ShapeIt so not exactly a reference.

I am interested in phasing rare variants but the documentation says you only need to use ShapeIt phase_rare for a large number of samples. Does anyone understand the disparity?

Thanks so much in advance!!! Evan