Fast Ordered Sampling of DNA Sequence Variants

• Main Author: Anthony J. Greenberg
• Format: Article
• Language: English
• Published: Oxford University Press 2018-05-01
• Series: G3: Genes, Genomes, Genetics
• Subjects: nucleotide polymorphism; random sampling; statistical genetics; genomics; C++
• Online Access: http://g3journal.org/lookup/doi/10.1534/g3.117.300465

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.