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Calling all GATK-savvy developers: we're hiring! Aug 28

We're looking for a developer (software engineer or equivalent) to join our team on a part-time basis as a software engineering consultant.

The mission is to take on tasks that are non-critical but still important, such as fixing bugs and implementing minor feature requests, usability improvements and so on in the GATK codebase. The idea is to take much of the maintenance burden off of the core development team so they can focus on developing new tools and methods.

We already have one person employed in this capacity, and it's working out very well. However there is quite a bit more to do than he can find time for, and therefore we'd like to hire a second consultant to pick up the extra work in parallel. (We were hoping to just clone him but ran into some difficulties getting IRB approval.)

This position does not require expert knowledge of GATK, but familiarity with the GATK tools is a big plus. The main language is Java, with a small side of R and Scala. We also have a growing corpus of C++ code that is not yet in the scope of this position, but may move into scope some months down the line.

Note that this opportunity is amenable to remote work so you don't need to be local to the Boston area, but it is limited to US residents with valid work authorization (no H1B sponsorship possible, sorry).

Drop us a line in the comments below or private-message me (@Geraldine_VdAuwera) to discuss details.

Workshop announcement: Philadelphia, September 18-19 Aug 28

Here is the official announcement for the upcoming workshop in Philadelphia. Registration is not necessary for the lecture sessions, but it is required for the hands-on sessions (see link further below).

We look forward to seeing you there!


Any ploidy goes! Aug 27

Until now, HaplotypeCaller was only capable of calling variants in diploid organisms due to some assumptions made in the underlying algorithms. I'm happy to announce that we now have a generalized version that is capable of handling any ploidy you specify at the command line!

This new feature, which we're calling "omniploidy", is technically still under development, but we think it's mature enough for the more adventurous to try out as a beta test ahead of the next official release. We'd especially love to get some feedback from people who work with non-diploids on a regular basis, so we're hoping that some of you microbiologists and assorted plant scientists will take it out for a spin and let us know how it behaves in your hands.

It's available in the latest nightly builds; just use the -ploidy argument to give it a whirl. If you have any questions or feedback, please post a comment on this article in the forum.

Caveat: the downstream tools involved in the new GVCF-based workflow (GenotypeGVCFs and CombineGVCFs) are not yet capable of handling non-diploid calls correctly -- but we're working on it.

Appistry webinar on RNAseq analysis pipeline 8/21 Aug 15

Our partners at Appistry will be doing a webinar on RNAseq analysis next Thursday. The webinar will include a live presentation of the complete pipeline for RNAseq analysis, as well as question time open to all participants. As usual it's free and open to all, you just need to register at Appistry's website. Check it out!

Abstract for Genome Science UK (Oxford, Sept. 1-3) Aug 13

Here's my abstract for the upcoming Genome Science UK meeting in Oxford, where I'll be talking about our hot new workflow for variant discovery. The slide deck will be posted in the Presentations section as usual after the conference.


Version highlights for GATK version 3.2 Jul 30

Better late than never (right?), here are the version highlights for GATK 3.2. Overall, this release is essentially a collection of bug fixes and incremental improvements that we wanted to push out to not keep folks waiting while we're working on the next big features. Most of the bug fixes are related to the HaplotypeCaller and its "reference confidence model" mode (which you may know as -ERC GVCF). But there are also a few noteworthy improvements/changes in other tools which I'll go over below.


Appistry Pipeline Contest Jul 23

Creative minds, your attention please -- our licensing partners, Appistry, are holding a competition! From the Appistry Pipeline Challenge webpage:

The Appistry Pipeline Challenge will reward and support one winning proposal for a creative pipeline that will make a difference in clinical research and precision medicine. We’ll provide the winner with a complete NGS analysis package valued at $70,000 including commercial-grade bioinformatics tools for variant calling and somatic mutation analysis, software and hardware for developing and executing pipelines at scale, and a year’s worth of support so that you can make your idea a reality.

There's more detailed information on the contest webpage of course, and if that doesn't answer all your questions, Appistry is holding a live webinar tomorrow (Thursday 7/24) to give additional details and answer questions.

The deadline for submissions is August 15th, so if you have an idea, better get on it!

Release notes for GATK version 3.2 Jul 15

GATK 3.2 was released on July 14, 2014. Highlights are listed below. Read the detailed version history overview here:


Tue 15 Jul 2014

Meetings, workshops, conferences, oh my! (carbon footprint) Jul 2

Ladies, gentlemen and everyone else (this is a judgment-free zone), it's officially summertime in the norther hemisphere. Depending on who and where you are, this can mean no more classes, no more exams, and more quality time with your loved ones -- or extra expense getting someone to keep your offspring out of your way (hello summer camp). It is that hallowed time of year when academics put down the burdens of teaching and administrative duties and can finally get some science done. For many, it also means conference season, e.g. meeting up in Spain with a bunch of colleagues to argue about obscure methodological details over many a glass of tinto de verano. It's a hard, hard life.

A group of us just got back from sunny Belgium* where we held a GATK workshop at the invitation of the Royal Institute for Natural Sciences in Brussels. Now we're looking ahead to the next big dates on the horizon, and I thought I'd share them here in case some of you can join us. Or in case you would like to invite us over to give talks or workshops... (seriously, private-message me if you're interested in hosting a GATK workshop).

* This is not irony, it was really beautiful the whole time. Until the two non-Belgians left, and then boom! Downpour for three days. Typical.

As you can see below, our dance card is all clear for the summer itself but starting September it gets pretty busy.


Slides from the June 2014 GATK workshop in Brussels, Belgium Jun 25

The presentation slides are available on DropBox at this link:

After the workshop, these materials as well as the hands-on tutorial will be posted in the Presentations section of the website.

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GATK Dev Team


RT @KAngevi: Curious about how much faster GATK 3 is vs. GATK 2?? Check out my blog entry! #Appistry
28 Aug 14
We're hiring! Looking for a developer to join us on a part-time basis to fix bugs. Remote OK but USA only.
28 Aug 14
Upcoming #GATK workshop at UPenn in Philadelphia, September 18-19, details at
28 Aug 14
We have a new favorite for best "meaning of SNP" answer: Still No Paper !
27 Aug 14
Any ploidy goes! New #GATK HaplotypeCaller feature available for beta testing.
27 Aug 14