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    Benchmarking small-variant genotyping in polyploids

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    Genome Res.-2021-Cooke-gr.2755 ...
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    Authors
    Cooke, D. P.
    Wedge, D. C.
    Lunter, G.
    Issue Date
    2022
    
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    Abstract
    Genotyping from sequencing is the basis of emerging strategies in the molecular breeding of polyploid plants. However, compared with the situation for diploids, in which genotyping accuracies are confidently determined with comprehensive benchmarks, polyploids have been neglected; there are no benchmarks measuring genotyping error rates for small variants using real sequencing reads. We previously introduced a variant calling method, Octopus, that accurately calls germline variants in diploids and somatic mutations in tumors. Here, we evaluate Octopus and other popular tools on whole-genome tetraploid and hexaploid data sets created using in silico mixtures of diploid Genome in a Bottle (GIAB) samples. We find that genotyping errors are abundant for typical sequencing depths but that Octopus makes 25% fewer errors than other methods on average. We supplement our benchmarks with concordance analysis in real autotriploid banana data sets.
    Citation
    Cooke DP, Wedge DC, Lunter G. Benchmarking small-variant genotyping in polyploids. Vol. 32, Genome Research. Cold Spring Harbor Laboratory; 2021. p. 403–8.
    Journal
    Genome Research
    URI
    http://hdl.handle.net/10541/625089
    DOI
    10.1101/gr.275579.121
    Additional Links
    https://dx.doi.org/10.1101/gr.275579.121
    Type
    Article
    Language
    en
    ae974a485f413a2113503eed53cd6c53
    10.1101/gr.275579.121
    Scopus Count
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    All Paterson Institute for Cancer Research

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