Service note: forum on break, support resumes Nov 27
Today in the US we're celebrating the national "Stuffing Your Face" holiday known as Thanksgiving, and we get the day off tomorrow to recover, so the forum is going to be unattended until Monday Nov 27.
So whether you're in the US and looking for an escape from your in-laws, or you're in some other part of the world and waiting for an answer to your pressing GATK question... Why not take a break, slip away for a bit and read the HaplotypeCaller paper, which is finally out in preprint form on bioarxiv here, under the title "Scaling accurate genetic variant discovery to tens of thousands of samples".
Or do both us and yourself a favor by filling in our GATK survey and winning one of the 100 prizes we're giving away! Seriously, we have a whole bunch of $50 Amazon gift cards (which you can get in your local currency if you live outside the USA) and prizes of up to $500 compute credits to spend in FireCloud, our cloud-based analysis platform. You can read more about the goal of the survey here.