Minimizing reference bias with an imputed personalized reference.

Abstract excerpt

Pangenome indexes reduce reference bias in sequencing data analysis. However, bias can be reduced further by using a personalized reference, for example, a diploid human reference constructed to match a donor individual's alleles. Here, we present a new impute-first alignment framework that combines elements of genotype imputation and read alignment. We first genotype the individual using a subsample of the input...

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