The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
Let's play GATK Survivor: what tools will get voted off the island?
Warning: the following content may shock or distress our more sensitive users, as we discuss the cold-blooded elimination of some tools from the GATK.
Alright, now that I've got your attention (hopefully -- if not, what does it take?), here's the deal. We have got to a point where the GATK is a widely, even massively used toolkit (thanks to you, dear users). And it's pretty darn robust -- it's what the Broad's Genomic Platform uses in production to churn out exomes like there's no tomorrow. But it has technical limitations that are 1) a frequent source of pain on your end and 2) increasingly hampering development of new methods on our end.
The good news is that we have a plan for addressing (read: blasting away) these limitations. But part of this plan will involve streamlining GATK by getting rid of tools that are not useful or are inferior to alternative tools from other packages that we're not trying to compete with (e.g. Picard tools).
Some tools that are safe from elimination: all the tools used in the Best Practices, and a couple of utilities that we use a lot ourselves. But everything else is up for review -- and that's where you come in: we need your input to decide what to keep, what to throw away, and what to consider rewriting from scratch (yep, this is an option).
This link will take you to a SurveyMonkey page that lists the tools currently on the chopping block:
Act now to save your favorite non-BP tools! Or help us get rid of the crud. Whichever way you want to look at it, we appreciate your feedback!