Reference-based Phasing of Chromosome X using Eagle

Question

[Mohadese]

Hi,

I want to perform referenced-based phasing on chromosome X using eagle. Do I need to separate PAR, and Non-PAR regions of chromosome X to do so or does Eagle support phasing the whole chromosome simultaneously?

Answer 1

[4galaxy77]

Try using EalgeImp:

To allow phasing and imputation for very large reference panels, while ensuring at least the same phasing and imputation accuracy, we developed EagleImp, a software tool for accelerated phasing and imputation. EagleImp introduces algorithmic and implementation improvements to the established tools Eagle2 [2] (phasing) and PBWT [3] (imputation) in a single convenient application.

....

In addition, EagleImp supports imputation of chromosome X and Y with automatic partitioning by pseudo-autosomal regions (PAR).

[Mohadese]

I need to replicate TOPMed imputation server tools. They use Eagle for reference based phasing and minimac for imputation.

[4galaxy77]

Ok, please try mention all your details in the original question so people don’t waste time giving you incorrect advice. This should answer your question anyway Problems Imputing X Chromosome with TOPMed