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?
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Mohadese •
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.
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In addition, EagleImp supports imputation of chromosome X and Y with automatic partitioning by pseudo-autosomal regions (PAR).
I need to replicate TOPMed imputation server tools. They use Eagle for reference based phasing and minimac for imputation.
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
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