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Bioinformatics Advance Access originally published online on May 20, 2008
Bioinformatics 2008 24(14):1645-1646; 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 and 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.


  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

Contact: tsunoda{at}src.riken.jp

Supplementary information: Additional materials can be found at http://emu.src.riken.jp/MOCSphaser/SuppInfor.doc

Associate Editor: Martin Bishop

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

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