There are a few ways to export data from the Illumina BeadStudio Data Analysis Software application for analysis in HelixTree. Genotype data can be exported using BeadStudio’s Final Report feature. Copy number intensity data can be exported using BeadStudio’s Custom Report feature and HelixTree’s custom plug-ins. In both cases there are options that must be set to insure the data will import properly into HelixTree. This chapter will outline those requirements.