Filtering "noisy" reads

jstjohn

Hello, 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? Thanks, John

Geraldine_VdAuwera

Hi there,

You may want to ask this directly to the author of MuTect, who answers questions here:

http://gatkforums.broadinstitute.org/categories/mutect

jstjohn

Thanks, I posted the question in the MuTect form. Maybe after I find out what is meant by a noisy read I'll be back here to find out how to do it though. :)