ParaHaplo: A program package for haplotype-based whole-genome association study using parallel computing.

ABSTRACT:

Background

Since more than a million single-nucleotide polymorphisms (SNPs) are analyzed in any given genome-wide association study (GWAS), performing multiple comparisons can be problematic. To cope with multiple-comparison problems in GWAS, haplotype-based algorithms were developed to correct for multiple comparisons at multiple SNP loci in linkage disequilibrium. A permutation test can also control problems inherent in multiple testing; however, both the calculation of exact probability and the execution of permutation tests are time-consuming. Faster methods for calculating exact probabilities and executing permutation tests are required.

Methods

We developed a set of computer programs for the parallel computation of accurate P-values in haplotype-based GWAS. Our program

SUBMITTER: Misawa K 

PROVIDER: S-EPMC2774321 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature