parallelGWAS

parallelGWAS accelerates genotype imputation and haplotype reconstruction for genome-wide association studies (GWAS) on large-scale single nucleotide polymorphism (SNP) datasets using parallel computation on Intel Message Passing Interface (MPI) workstation clusters.

Key Features:

• Parallel Computing: Leverages parallel computation optimized for workstation clusters using the Intel Message Passing Interface (MPI) to process large-scale single nucleotide polymorphism (SNP) datasets for genotype imputation and haplotype reconstruction.
• Performance: Performs genotype imputation up to 20 times faster than non-parallel counterparts.

Scientific Applications:

• Haplotype-based GWAS: Used for haplotype-based GWAS.
• Validation on diverse datasets: Validated on datasets including Japanese individuals in Tokyo, Han Chinese populations in Beijing, and the HapMap dataset.

Methodology:

Models linkage disequilibrium patterns within a reference panel to predict unmeasured genotypes in study samples and performs haplotype reconstruction to fill gaps in genotype data.