Creating lists of shared regions can be described as the core step of the copy number analysis in a project with multiple samples/patients. For example, lists could be created containing all the deleted regions on chromosome 4, all the regions spanning more than 50000 bp, or all the regions containing a certain number of markers, depending on the experimental question being asked. In this exercise, all the samples have same underlying phenotype, and two lists will be created: In this tutorial, the experimental goal is to identify regions with copy number changes in multiple patients. To do this, we will create a list containing deleted and amplified regions across the genome shared by 8 or more samples. 

• Select Create Region List from the Copy Number Analysis section of the Copy Number workflow
• Select Specify New Criteria 

The criteria we We want to create will include all the amplified regions across the genome shared by at least 8 samples in our first criteria (Figure 1). 

• Set Name to Amplified
• Set Spreadsheet to 2/segmentation/summary (segment-analysis) 
• Set Column to 6. Total Amplifications using the drop-down menu
• Deselect the box next to Include values less than or equal to
• Set Include values greater than or equal to value to 8

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