Our partner Appistry (who distribute GATK and MuTect to commercial users) will be holding a webinar on 3 October. Registration is open to all; you can find more details on the Appistry website here:
Heads up, cancer researchers! Appistry (our commercial licensing partner for GATK and now MuTect) is announcing an upcoming webinar on best practices for somatic mutation studies using GATK and MuTect. Registration for the webinar is open to all (not just Appistry customers) so be sure to sign up for this. See the announcement on Appistry's website for more detailed information.
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