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Research Article

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

  • Bryan N. Howie,

    Affiliation: Department of Statistics, University of Oxford, Oxford, United Kingdom

    Current address: Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America

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  • Peter Donnelly,

    Affiliations: Department of Statistics, University of Oxford, Oxford, United Kingdom, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, United Kingdom

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  • Jonathan Marchini mail

    marchini@stats.ox.ac.uk

    Affiliation: Department of Statistics, University of Oxford, Oxford, United Kingdom

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  • Published: June 19, 2009
  • DOI: 10.1371/journal.pgen.1000529

Reader Comments (4)

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BEAGLE memory usage

Posted by SharonBrowning on 16 Jul 2009 at 14:26 GMT

While BEAGLE was quite fast, it also required more than ten times as much RAM as any other method (at least 2.5 GB per 7.5 Mb region of the genome).
http://plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000529#article1.body1.sec3.sec2.sec6.p2

BEAGLE's memory requirements flatten out as the region size increases. In our experience, BEAGLE will perform imputation in the same set of samples in a 245 Mb region (all of chromosome 1) using 3 GB of memory with default options, and 2 GB of memory with the low memory option.

No competing interests declared.

RE: BEAGLE memory usage

tommycarstensen replied to SharonBrowning on 11 Mar 2013 at 10:43 GMT

I have used BEAGLE on fragments of 5000-45000 markers. Using the lowmem option I have observed max memory usage between ~1000MB and ~3100MB, which is independent of the size of the fragment. IMPUTE2 seems to require ~5100MB of RAM per 100k markers.

No competing interests declared.