Forum: Are you using GATK ?
2
gravatar for tiffanym
2.2 years ago by
tiffanym20
tiffanym20 wrote:

As many of you know, GATK4 Beta is out and we [Broad Team] are excited for the full GATK4 to be released January 9th, 2018. It has been a long time coming and we hope that many of you have gotten to experiment with its features before the big release. In fact, we’d like to know if you’ve tried it out!

We crafted a survey that asks questions about your experience with GATK, the Beta release, thoughts on the upcoming GATK4 release and the infrastructure you run on to help improve our team’s communication, support, and product development efforts. If you have not used the Beta or do not know much about GATK4, please tell us in this survey, as that is very useful for us to know. This survey is for anyone who has ever used any GATK version.

The Survey: https://www.surveymonkey.com/r/GATK_survey

The survey is 27 questions long and should take 10 minutes to complete. We want to compensate you for your time so we have gotten some reward funding from the Intel Center for Genomic Data Engineering, established at the Broad Institute in 2017.

We will randomly draw 100 survey participants and offer each winner one prize of their choosing:

In the survey, we ask that you leave your contact email and rank the prizes in the order you’d like to receive them. We will allocate them as we randomly draw winners. This means if we have run out of FireCloud credit and you are the sixth person who put this as your number one choice, we will allocate you your second choice. The survey will be live for one month.

We know that everyone is busy with their work and we think that these gifts and the action your feedback will generate is worth the ten minutes spared. The FireCloud credit reward could even go into funding your research! Whether you win something or not, your feedback is used for a greater purpose - your opinions will help the Broad team and the collaborators at the Intel Center learn how to improve the GATK communities’ experience by understanding its needs.

Thank you for reading & good luck!

Tiffany Miller

tiffanym [@] broadinstitute.org

Note on prizes: Amazon gift cards will be issued for use in your home country.

forum gatk gatk4 • 1.0k views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by tiffanym20

Excited for GATK4! The Spark learning curve bothers me a little though - it is moving to Spark, right? Will this also be plugging in to hail?

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by RamRS25k

You're right that GATK4 includes support for Spark, but that doesn't mean you now need to learn Spark as such. If you're using GATK4 on "normal" machines (ie not on a Spark cluster) you don't actually need to know anything about Spark. The multithreading will kick in if your machine supports it, but you don't need to do anything to control it explicitly (unless you want to tweak settings, and even there the parameterization should be fairly straightforward). Where it can get a bit more complicated is if you're running on a Spark cluster (or a service like Google Dataproc) because there you need to make some decisions about how to utilize your cluster most effectively. We'll try to provide documentation to help you use this without tearing your hair out.

There is no direct connection to Hail at the moment but we plan to work with the Hail team to facilitate the transition from the GATK side of the work to the Hail side.

ADD REPLYlink written 2.2 years ago by vdauwera960

That's wonderful! I'm trying to get to a place where I can spin off a bunch of nodes on AWS and use GATK on them efficiently. It would be great to have some documentation on how to get a cloud equivalent of Queue up and running.

ADD REPLYlink written 2.2 years ago by RamRS25k

See our WDL + Cromwell pipelining solution for that, which replaces Queue. It runs on several platforms out of the box, including Google Cloud; we’re working on making it run on AWS. If you’re not married to AWS I can point you to the docs for running on Google. We also have an analysis service set up on Google called FireCloud that makes it even easier; it’s free to access, you just pay Google for storage and compute costs.

ADD REPLYlink written 2.2 years ago by vdauwera960

I don't think it makes sense to be particular about AWS, unless Google proves too expensive. I'd appreciate that pointer to the docs for running GATK4 on Google Cloud - thank you! :-)

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by RamRS25k
1

Whoops, sorry I forgot to answer you! If you swing by the GATK website on Jan 9 you will find all the information you ever wanted ;)

In the meantime, FYI we got some funding to offer $250 worth of compute credits to anyone who wants to try GATK4 workflows on FireCloud, more details here: https://software.broadinstitute.org/gatk/blog?id=11002

ADD REPLYlink written 2.1 years ago by vdauwera960
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