title: Compression and fast retrieval of SNP data.
abstract: BACKGROUND
  The increasing interest in rare genetic variants and epistatic genetic effects on complex phenotypic traits is currently pushing genome-wide association study design towards datasets of increasing size, both in the number of studied subjects and in the number of genotyped single nucleotide polymorphisms (SNPs). This, in turn, is leading to a compelling need for new methods for compression and fast retrieval of SNP data.
  
  
  RESULTS
  We present a novel algorithm and file format for compressing and retrieving SNP data, specifically designed for large-scale association studies. Our algorithm is based on two main ideas: (i) compress linkage disequilibrium blocks in terms of differences with a reference SNP and (ii) compress reference SNPs exploiting information on their call rate and minor allele frequency. Tested on two SNP datasets and compared with several state-of-the-art software tools, our compression algorithm is shown to be competitive in terms of compression rate and to outperform all tools in terms of time to load compressed data.
  
  
  METHODS
  Our compression and decompression algorithms are implemented in a C++ library, are released under the GNU General Public License and are freely downloadable from http://www.dei.unipd.it/~sambofra/snpack.html.
authors: Department of Information Engineering, University of Padova, via Gradenigo 6/a, 35131 Padova, Italy.
authors: Francesco
authors: F
authors: Sambo
authors: Department of Information Engineering, University of Padova, via Gradenigo 6/a, 35131 Padova, Italy.
authors: Barbara
authors: B
authors: Di Camillo
authors: Department of Information Engineering, University of Padova, via Gradenigo 6/a, 35131 Padova, Italy.
authors: Gianna
authors: G
authors: Toffolo
authors: Department of Information Engineering, University of Padova, via Gradenigo 6/a, 35131 Padova, Italy.
authors: Claudio
authors: C
authors: Cobelli
mesh_terms: D000465:Algorithms; D044962:Data Compression / Q000379:methods*; D005787:Gene Frequency; D055106:Genome-Wide Association Study; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D012984:Software