README.txt

Use scripts and notes from Week 6 practical (https://github.com/papenfuss/BINF90004) to process the provided sequenza files and determine changes in copy number in primary (CA0023-61-2 & CA0023-61-3) and metastatic liver (CA0023-65 & CA0023-66) tumors when compared to the germ line controls. Based on the changes in copy number, manually reconstruct the evolutionary relationship of these samples as a phylogenetic tree. Not all diagnostic plots used in the practical session need to be embedded in the scientific report. However, the steps used to plot all figures should be included in the materials and methods and annotated scripts to show that you have explored the data before conducting the copy number variation analysis (using the sequenza R package).