How can I use GATK to identify mutation hotspots on a genome? What tools do I use? I have an organism that I UV mutagenized and resequenced and now I want to identify regions on the genome that were more prone to mutation.
GATK can only give you the mutations themselves. To do an analysis on mutation hotspots you will need to use some other software, I recommend looking in the literature to see what people use for this. Good luck!