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


BACKGROUND
http://emu.src.riken.jp/MOCSphaser/MOCSphaser.zip.
Kato
Mamoru
M
SNP Research Center, RIKEN, 1-7-22 Suehiro, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Nakamura
Yusuke
Y
Tsunoda
Tatsuhiko
T
D000465:Algorithms; D000483:Alleles; D019295:Computational Biology / Q000379:methods*; D018628:Gene Dosage; D005787:Gene Frequency; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D010641:Phenotype; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D012984:Software