Current software for genotype imputation
<p>Abstract</p> <p>Genotype imputation for single nucleotide polymorphisms (SNPs) has been shown to be a powerful means to include genetic markers in exploratory genetic association studies without having to genotype them, and is becoming a standard procedure. A number of different...
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doaj-f35fff4c6c33416395a2e818965c71f62020-11-24T20:41:59ZengBMCHuman Genomics1479-73642009-07-013437138010.1186/1479-7364-3-4-371Current software for genotype imputationEllinghaus DavidSchreiber StefanFranke AndreNothnagel Michael<p>Abstract</p> <p>Genotype imputation for single nucleotide polymorphisms (SNPs) has been shown to be a powerful means to include genetic markers in exploratory genetic association studies without having to genotype them, and is becoming a standard procedure. A number of different software programs are available. In our experience, user-friendliness is often the deciding factor in the choice of software to solve a particular task. We therefore evaluated the usability of three publicly available imputation programs: BEAGLE, IMPUTE and MACH. We found all three programs to perform well with HapMap reference data, with little effort needed for data preparation and subsequent association analysis. Each of them has different strengths and weaknesses, however, and none is optimal for all situations.</p> http://www.humgenomics.com/content/3/4/371genotype imputation softwaregenome-wide association studyHapMapsingle nucleotide polymorphism |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ellinghaus David Schreiber Stefan Franke Andre Nothnagel Michael |
spellingShingle |
Ellinghaus David Schreiber Stefan Franke Andre Nothnagel Michael Current software for genotype imputation Human Genomics genotype imputation software genome-wide association study HapMap single nucleotide polymorphism |
author_facet |
Ellinghaus David Schreiber Stefan Franke Andre Nothnagel Michael |
author_sort |
Ellinghaus David |
title |
Current software for genotype imputation |
title_short |
Current software for genotype imputation |
title_full |
Current software for genotype imputation |
title_fullStr |
Current software for genotype imputation |
title_full_unstemmed |
Current software for genotype imputation |
title_sort |
current software for genotype imputation |
publisher |
BMC |
series |
Human Genomics |
issn |
1479-7364 |
publishDate |
2009-07-01 |
description |
<p>Abstract</p> <p>Genotype imputation for single nucleotide polymorphisms (SNPs) has been shown to be a powerful means to include genetic markers in exploratory genetic association studies without having to genotype them, and is becoming a standard procedure. A number of different software programs are available. In our experience, user-friendliness is often the deciding factor in the choice of software to solve a particular task. We therefore evaluated the usability of three publicly available imputation programs: BEAGLE, IMPUTE and MACH. We found all three programs to perform well with HapMap reference data, with little effort needed for data preparation and subsequent association analysis. Each of them has different strengths and weaknesses, however, and none is optimal for all situations.</p> |
topic |
genotype imputation software genome-wide association study HapMap single nucleotide polymorphism |
url |
http://www.humgenomics.com/content/3/4/371 |
work_keys_str_mv |
AT ellinghausdavid currentsoftwareforgenotypeimputation AT schreiberstefan currentsoftwareforgenotypeimputation AT frankeandre currentsoftwareforgenotypeimputation AT nothnagelmichael currentsoftwareforgenotypeimputation |
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