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

ABSTRACT:

Unlabelled

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.

SUBMITTER: Kato M

PROVIDER: S-EPMC2638261 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature

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

Kato Mamoru M Nakamura Yusuke Y Tsunoda Tatsuhiko T

Bioinformatics (Oxford, England) 20080520 14

<h4>Unlabelled</h4>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 ...[more]

PMID: 18492685

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