famCNV: copy number variant association for quantitative traits in families

famCNV is a user-friendly Java program that enables genome-wide association of copy number variants with quantitative phenotypes in families of arbitrary size and complexity. It uses intensity signals such as the log ratio of observed to expected signal intensity (LRR) from Illumina genotyping arrays.

The quantitative trait of interest is analysed in a variance component framework to model the resemblance among relatives and to remove possible bias from familiarity.

famCNV is now at version 2.0. This new version allows a more flexible input, and quantile normalisation can be automatically applied to each phenotype to improve normality of the response variables. Moreover, its output includes also beta and percentage of variance explained. The significance of the results is also now tested both through formal likelihood testing and through an empirical adaptive procedure. Version 2.0 is also more efficient in its implementation, allowing multithreading.