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Filtering "noisy" reads

jstjohnjstjohn Member Posts: 3

From a talk on MuTect from a while ago, I found a reference to filtering out "noisy" reads. This seems like a great idea, and I would like to do it for other standard GATK based variant calling as well. How exactly do you do this kind of "noisy read" filtering. From the graphic in the talk, it looks like reads with a lot of mismatches relative to the others in a region, after indel realignment are candidates for being these kind of noisy reads. How is this defined exactly though, and how could I do something similar with GATK?

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