ParaHaplo 2.0: a program package for haplotype-estimation and haplotype-based whole-genome association study using parallel computing

doi:10.1186/1751-0473-5-5

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Software review

ParaHaplo 2.0: a program package for haplotype-estimation and haplotype-based whole-genome association study using parallel computing

Kazuharu Misawa¹ and Naoyuki Kamatani²

¹Research Program for Computational Science, Research and Development Group for Next-Generation Integrated Living Matter Simulation, and Fusion of Data and Analysis Research and Development Team, RIKEN, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan

²Laboratory for Statistical Analysis, RIKEN Center for Genomic Medicine, Tokyo, Japan

author email corresponding author email

Source Code for Biology and Medicine 2010, 5:5doi:10.1186/1751-0473-5-5


Published:	4 June 2010

Abstract

Background

The use of haplotype-based association tests can improve the power of genome-wide association studies. Since the observed genotypes are unordered pairs of alleles, haplotype phase must be inferred. However, estimating haplotype phase is time consuming. When millions of single-nucleotide polymorphisms (SNPs) are analyzed in genome-wide association study, faster methods for haplotype estimation are required.

Methods

We developed a program package for parallel computation of haplotype estimation. Our program package, ParaHaplo 2.0, is intended for use in workstation clusters using the Intel Message Passing Interface (MPI). We compared the performance of our algorithm to that of the regular permutation test on both Japanese in Tokyo, Japan and Han Chinese in Beijing, China of the HapMap dataset.

Results

Parallel version of ParaHaplo 2.0 can estimate haplotypes 100 times faster than a non-parallel version of the ParaHaplo.

Conclusion

ParaHaplo 2.0 is an invaluable tool for conducting haplotype-based genome-wide association studies (GWAS). The need for fast haplotype estimation using parallel computing will become increasingly important as the data sizes of such projects continue to increase. The executable binaries and program sources of ParaHaplo are available at the following address: http://en.sourceforge.jp/projects/parallelgwas/releases/ webcite