Does Beagle use the reference genome for both phasing AND imputing genotypes?
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!
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giulia.trauzzi •
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