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Beyond Bioinformatics | |
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Title |
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HapMap filter 1.0: A tool to preprocess the HapMap genotypic data for association studies
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Authors |
Wei Zhang1, Shiwei Duan1 and M. Eileen Dolan1, 2, 3, *
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Affiliation |
1Section of Hematology/Oncology, Department of Medicine; 2Committee onClinical Pharmacology and Pharmacogenomics; 3Cancer Research Center, The University of Chicago, IL 60637, USA
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edolan@medicine.bsd.uchicago.edu
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773 702 4441
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773 702 0963; * Corresponding author
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Article Type |
Software
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Date |
received April 29, 2008; accepted May 06, 2008; published May 13, 2008 | ||||||||||||||||||||||||||||
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Abstract |
The International HapMap Project provides a resource of genotypic data on single nucleotide polymorphisms (SNPs), which can be used in various association studies to identify the genetic determinants for phenotypic variations. Prior to the association studies, the HapMap dataset should be preprocessed in order to reduce the computation time and control the multiple testing problem. The less informative SNPs including those with very low genotyping rate and SNPs with rare minor allele frequencies to some extent in one or more population are removed. Some research designs only use SNPs in a subset of HapMap cell lines. Although the HapMap website and other association software packages have provided some basic tools for optimizing these datasets, a fast and user-friendly program to generate the output for filtered genotypic data would be beneficial for association studies. Here, we present a flexible, straight-forward bioinformatics program that can be useful in preparing the HapMap genotypic data for association studies by specifying cell lines and two common filtering criteria: minor allele frequencies and genotyping rate. The software was developed for Microsoft Windows and written in C++.
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| Availability |
The Windows executable and source code in Microsoft Visual C++ are available at Google Code (http://hapmap-filter-v1.googlecode.com/) or upon request. Their distribution is subject to GNU General Public License v3.
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Keywords |
HapMap; genotype; single nucleotide polymorphism; minor allele frequency; genotyping rate
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Citation |
W. Zhang et al., Bioinformation 2(8): 322-324 (2008)
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Edited by |
P. Kangueane
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ISSN |
0973-2063
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Publisher |
Biomedical Informatics Publishing Group
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Copyright |
Publisher
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Copyright Transfer Agreement |
The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.
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License |
This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
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