MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.
basic_science · Level V
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- Record sourced from PubMed, PMID 18492685.
- Also identified by DOI 10.1093/bioinformatics/btn242 and PMC identifier 2638261.
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Abstract
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. http://emu.src.riken.jp/MOCSphaser/MOCSphaser.zip.
Medical subject headings
- Computational Biology
- Haplotypes
- Polymorphism, Single Nucleotide