CNVice

CNVice (Inbreeding Coefficients Estimation for CNV data) is a freely available R script for population genetics applications.

CNVice performs the following analyses:

1. Estimates allele frequencies for a given population assuming Hardy-Weinberg equilibrium (HWE), using the expectation maximization algorithm as implemented in CoNVEM (Gaunt et al. 2010), conditioning on the observed diplotype frequencies.
2. Estimates the population structure parameter _CNV and allele frequencies, using the profiled likelihood function and the Expectation Maximization (EM) algorithm (Severini 2000)
3. Estimates the population genotype frequency, conditioning on the observed diplotype distribution and the estimated f_CNV and allele frequencies.
4. Uses trio information to improve the inference of an offspring’s genotype, by considering the parents’ diplotypes and the population genotype frequency.

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