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Hidden copy number variation in the HapMap trios

John C. Marioni, Michael White, Simon Tavaré and Andrew G. Lynch

 

This page contains the data and code necessary to perform the calculations described in the above paper that was submitted to PNAS.

The data described in Supplementary Table 1, which were used to calculate the likelihood, were derived from the mixture-model based CNV classifications described by Marioni et al. (Genome Biology, in press).

The R code needed to calculate the likelihood of observing the summarized data for the 90 Yoruban samples (Supplementary Table 1), and the bootstrap-generated confidence intervals contained in Supplementary Table 2, is available here.

The code used to generate the updated classifications described in Table 2, as well as the necessary input data objects are contained in NewCalls.zip. Note that, to run this code, it will first be necessary to install the snapCGH BioConductor library. This can be downloaded from the BioConductor website. Finally, some additional information about the formulae used to update the classifications is provided here.

For further details please contact Dr. John Marioni