RT Journal Article
SR Electronic
T1 Fast ordered sampling of DNA sequence variants
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 220871
DO 10.1101/220871
A1 Greenberg, Anthony J.
YR 2017
UL http://biorxiv.org/content/early/2017/11/17/220871.abstract
AB 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.