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UV mutagenesis hotspots

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.

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    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!

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