Figure 1
From: CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations
Workflow of CNAReporter, describing sample input files, functions of CNAReporter modules and output examples. Specifically, areas of significant genomic change are tabulated in a PDF-file, characterized by its corresponding type, such as chromosomal gain, loss and allelic imbalances and linked to UCSC Genome Browser [20]. Furthermore, the patient specific report includes a genomic profile that provides raw and smoothed profiles of log2 ratios of sample to reference intensities representing copy numbers, areas of loss-of-heterozygosity (LOH) and genomic calls. These areas are finally labelled in a plot of chromosomal changes that are optionally available for each chromosome separately.