I have been using CNVkit to analyze my BAM files, and the outcome looks like this:
Is there any way to highlight a certain gene in this CNVkit output graph, or do I have to pipe this output segmentation file into another tool to do so? I would like to highlight the exact gene, but a vertical line on where it is would be fine as well. Any suggestions?
You can use the scatter command with one or more gene names to show those genes on a single chromosome. To generate plots for genes on multiple chromosomes, I recommend looping over your call set (e.g. genemetrics or .cns grouped by chromosome) to run scatter separately for each one. CNVkit won't label the whole-gene scatter plot.
The diagram command will show altered genes across the whole genome; it looks all right for target panels but gets cluttered for whole exomes.
