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ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing
BACKGROUND: Use of missing genotype imputations and haplotype reconstructions are valuable in genome-wide association studies (GWASs). By modeling the patterns of linkage disequilibrium in a reference panel, genotypes not directly measured in the study samples can be imputed and used for GWASs. Sinc...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123186/ https://www.ncbi.nlm.nih.gov/pubmed/21609440 http://dx.doi.org/10.1186/1751-0473-6-10 |
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author | Misawa, Kazuharu Kamatani, Naoyuki |
author_facet | Misawa, Kazuharu Kamatani, Naoyuki |
author_sort | Misawa, Kazuharu |
collection | PubMed |
description | BACKGROUND: Use of missing genotype imputations and haplotype reconstructions are valuable in genome-wide association studies (GWASs). By modeling the patterns of linkage disequilibrium in a reference panel, genotypes not directly measured in the study samples can be imputed and used for GWASs. Since millions of single nucleotide polymorphisms need to be imputed in a GWAS, faster methods for genotype imputation and haplotype reconstruction are required. RESULTS: We developed a program package for parallel computation of genotype imputation and haplotype reconstruction. Our program package, ParaHaplo 3.0, is intended for use in workstation clusters using the Intel Message Passing Interface. We compared the performance of ParaHaplo 3.0 on the Japanese in Tokyo, Japan and Han Chinese in Beijing, and Chinese in the HapMap dataset. A parallel version of ParaHaplo 3.0 can conduct genotype imputation 20 times faster than a non-parallel version of ParaHaplo. CONCLUSIONS: ParaHaplo 3.0 is an invaluable tool for conducting haplotype-based GWASs. The need for faster genotype imputation and haplotype reconstruction using parallel computing will become increasingly important as the data sizes of such projects continue to increase. ParaHaplo executable binaries and program sources are available at http://en.sourceforge.jp/projects/parallelgwas/releases/. |
format | Online Article Text |
id | pubmed-3123186 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-31231862011-06-25 ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing Misawa, Kazuharu Kamatani, Naoyuki Source Code Biol Med Software Review BACKGROUND: Use of missing genotype imputations and haplotype reconstructions are valuable in genome-wide association studies (GWASs). By modeling the patterns of linkage disequilibrium in a reference panel, genotypes not directly measured in the study samples can be imputed and used for GWASs. Since millions of single nucleotide polymorphisms need to be imputed in a GWAS, faster methods for genotype imputation and haplotype reconstruction are required. RESULTS: We developed a program package for parallel computation of genotype imputation and haplotype reconstruction. Our program package, ParaHaplo 3.0, is intended for use in workstation clusters using the Intel Message Passing Interface. We compared the performance of ParaHaplo 3.0 on the Japanese in Tokyo, Japan and Han Chinese in Beijing, and Chinese in the HapMap dataset. A parallel version of ParaHaplo 3.0 can conduct genotype imputation 20 times faster than a non-parallel version of ParaHaplo. CONCLUSIONS: ParaHaplo 3.0 is an invaluable tool for conducting haplotype-based GWASs. The need for faster genotype imputation and haplotype reconstruction using parallel computing will become increasingly important as the data sizes of such projects continue to increase. ParaHaplo executable binaries and program sources are available at http://en.sourceforge.jp/projects/parallelgwas/releases/. BioMed Central 2011-05-24 /pmc/articles/PMC3123186/ /pubmed/21609440 http://dx.doi.org/10.1186/1751-0473-6-10 Text en Copyright ©2011 Misawa and Kamatani; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Review Misawa, Kazuharu Kamatani, Naoyuki ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing |
title | ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing |
title_full | ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing |
title_fullStr | ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing |
title_full_unstemmed | ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing |
title_short | ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing |
title_sort | parahaplo 3.0: a program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing |
topic | Software Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123186/ https://www.ncbi.nlm.nih.gov/pubmed/21609440 http://dx.doi.org/10.1186/1751-0473-6-10 |
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