Does Beagle use the reference genome for both phasing AND imputing genotypes?
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11 days ago

Hi, I am phasing/imputing my genotypes and I am using Beagle. I am providing a reference genome for the imputation and I am not 100% confident that Beagle uses the reference panel (ref) for both phasing the genotypes and imputing them. I know it uses the ref for imputation but I was wondering if it also uses the same reference for phasing.

Anyone can confirm?

Thanks!

beagle genotypes phasing imputation • 265 views
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