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Fast ordered sampling of DNA sequence variants

View ORCID ProfileAnthony J. Greenberg
doi: https://doi.org/10.1101/220871
Anthony J. Greenberg
*Bayesic Research, Ithaca, NY, USA;
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Abstract

Explosive growth in the amount of genomic data is matched by increasing power of consumer-grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative samples from large data sets. I describe a fast and memory-efficient implementation of an on-line sampling method developed for tape drives 30 years ago. Focusing on genotype files, I test the performance of this technique on modern solid-state and spinning hard drives, and show that it performs well compared to a simple sampling scheme. I illustrate its utility by developing a method to quickly estimate genome-wide patterns of linkage disequilibrium (LD) decay with distance. I provide open-source software that samples loci from several variant format files, a separate program that performs LD decay estimates, and a C++ library that lets developers incorporate these methods into their own projects.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted November 17, 2017.
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Fast ordered sampling of DNA sequence variants
Anthony J. Greenberg
bioRxiv 220871; doi: https://doi.org/10.1101/220871
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Fast ordered sampling of DNA sequence variants
Anthony J. Greenberg
bioRxiv 220871; doi: https://doi.org/10.1101/220871

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