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Bioinformatics Advance Access published online on May 20, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn242
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data

Mamoru Kato 1, Yusuke Nakamura 1,2 and Tatsuhiko Tsunoda 1,*

1SNP Research Center, RIKEN, 1-7-22 Suehiro, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
2Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

*To whom correspondence should be addressed. Dr. Tatsuhiko Tsunoda, E-mail: tsunoda{at}src.riken.jp


  Abstract

Summary: Detailed analyses of the population-genetic nature of copy number variations (CNVs) and the linkage disequilibrium between CNV and single nucleotide polymorphism (SNP) loci from high-throughput experimental data require a computational tool to accurately infer alleles of CNVs and haplotypes composed of both CNV alleles and SNP alleles. Here we developed a new tool to infer population frequencies of such alleles and haplotypes from observed copy numbers and SNP genotypes, using the expectation-maximization algorithm. This tool can also handle copy numbers ambiguously determined, such as 2 or 3 copies, due to experimental noise.

Availability: http://emu.src.riken.jp/MOCSphaser/MOCSphaser.zip [Currently, a username "apple" and password "script" is required. We will remove this requirement after acceptance.]

Contact: kato{at}src.riken.jp

Supplementary information: Additional materials can be found at http://emu.src.riken.jp/MOCSphaser/SuppInfor.doc [Currently, a username "apple" and password "script" is required.

Associate Editor: Prof. Martin Bishop

Received on February 26, 2008; revised on April 26, 2008; accepted on May 19, 2008

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