MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data |
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Authors: | Kato Mamoru Nakamura Yusuke Tsunoda Tatsuhiko |
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Institution: | SNP Research Center, RIKEN, 1-7-22 Suehiro, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. |
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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. AVAILABILITY: http://emu.src.riken.jp/MOCSphaser/MOCSphaser.zip. |
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