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Achieving improved ...
Achieving improved accuracy for imputation of ancient DNA
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- Ausmees, Kristiina (författare)
- Uppsala universitet,Avdelningen för beräkningsvetenskap,Tillämpad beräkningsvetenskap
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- Nettelblad, Carl, 1985- (författare)
- Uppsala universitet,Avdelningen för beräkningsvetenskap,Tillämpad beräkningsvetenskap
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(creator_code:org_t)
- 2022-11-15
- 2023
- Engelska.
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Ingår i: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811. ; 39:1
- Relaterad länk:
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- MotivationGenotype 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.ResultsWe 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 lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU.
Ämnesord
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Matematik -- Beräkningsmatematik (hsv//swe)
- NATURAL SCIENCES -- Mathematics -- Computational Mathematics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Nyckelord
- Bioinformatics
- Computational biology
- Genotype imputation
- Ancient DNA
- Bioinformatics
- Bioinformatik
- Scientific Computing
- Beräkningsvetenskap
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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