Fast Ordered Sampling of DNA Sequence Variants

G3: Genes, Genomes, Genetics

Anthony J. Greenberg^1¹ 

[1] Bayesic Research, Ithaca, NY 14850^1

关键词: nucleotide polymorphism;    random sampling;    statistical genetics;    genomics;    C++;   

DOI  :  10.1534/g3.117.300465

学科分类：生物科学（综合）

来源: Genetics Society of America

【 摘 要 】

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.

【 授权许可】

CC BY