Dear GATK community,

I want to see if there is any GC coverage bias in exome data. I am using CollectMultipleMetrics with the -PROGRAM CollectGcBiasMetrics.

Is there any way to make the plot for exome data, like including target regions (I could not find this in the documentation or any flags for this). Since there seems to be a large GC coverage bias in my plot when you use it on exome data, ofcourse because I think you can only include the whole reference genome. So I presume the bias is caused by exome vs. genome.

Or can and should I just, for instance, use my target regions instead of the reference genome? I have read papers that use the CollectGcBiasMetrics on exome data and magically produce an unbiased plot (I say magically, because they say they use CollectGcBiasMetrics, but not how).

Any help/suggestions would be very welcome. Thank you in advance.

Figure for reference: