  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.
