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. 2008 May 20;24(14):1645–1646. doi: 10.1093/bioinformatics/btn242

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

Mamoru Kato 1, Yusuke Nakamura 1,2, Tatsuhiko Tsunoda 1,*
PMCID: PMC2638261  PMID: 18492685

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@src.riken.jp

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

Supplementary Material

[Supplementary Data]
btn242_index.html (756B, html)

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

[Supplementary Data]
btn242_index.html (756B, html)
btn242_bioinf-2008-0276-File002.doc (263KB, doc)

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