Achieving improved accuracy for imputation of ancient DNA.

ABSTRACT:

Motivation

Genotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data.

Results

We present an implementation called prophaser and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to

SUBMITTER: Ausmees K 

PROVIDER: S-EPMC9805568 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature