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

摘要

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.