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ASHG 2015 Poster: "Run smarter, not harder" Oct 8

Great poster session this morning at ASHG; Sheila and I got a lot of good questions about the Best Practices, and the GVCF workflow in particular. Our punchline: "This is how ExAC got done". It's super effective!

Preview of the poster after the fold. You can get the full-sized PDF here.


Countdown to ASHG 2015! Oct 4

Are you excited? We sure are. Especially in the secondary sense defined by as "stimulated to activity; brisk:". We're presenting a poster on Thursday and a 90-minute workshop on Friday, but neither is ready yet. Good thing the weather this weekend is crappy; if we were missing out on proper New England fall foliage / leaf-peeping weather we'd be pretty cheesed off.

But we ain't afraid of no deadline -- we'll be ready. We developed a completely new workshop tutorial for the occasion, and we're going to have a big room full of people rocking GVCFs. It's going to be epic. The tutorial data bundle, sans worksheet (because that's the part that's not quite ready yet) is already available here (not a direct link to the data because we want you to read the part about the homework). It does have an appendix document with installation instructions and some context info about the tutorial objectives, which you must read through (and act on) before the workshop, if you're attending.

If you're at ASHG but you can't make it to the workshop, you can still come see our poster, which covers the same topic (the GVCF workflow part of the Best Practices), but flatter and less interactive. Although Sheila and I will be there to answer questions one on one, so in that sense it will be more interactive. Just with less keyboard action. So, Thursday 9 Oct between 12 and 1 pm at the Bioinformatics and Genomic Technology session in the Exhibit Hall, Level 1; Convention Center, poster #1664/T. Be there. We'll talk.

We'll also be around at the Broad Institute Genomic Services booth in the Exhibit Hall (booth #1720, right around the corner from Qiagen). Not sure yet when we'll be there, but send me a private message if you'd like to chat and we can figure out a time.

See you there!

GATK workshop at ASHG 2015 Sep 18

We are scheduled to do a hands-on workshop at the ASHG 2015 meeting in Baltimore (see below for program details).

The workshop dataset and an appendix document containing detailed instructions for preparing for the workshop are now available for download at this link. The tutorial worksheet containing the actual exercises that we will do in the workshop is available for download here. Attendees will receive a printout of the worksheet at the workshop. We will not provide printouts of the appendix document.

If you are registered to attend, you must have downloaded the materials and followed the instructions before the workshop starts, otherwise you will not be able to follow along and your workshop experience will be unsatisfying. We certainly don't want that to happen, so be sure to do your homework as follows:

Get the files: 5 minutes

  • Download the 52 Mb zip file to the laptop you will bring to the workshop, and save it where you want the tutorial files to sit.
  • Open the zip file; this will create a directory called ASGH15_GATK.
  • Open the ASGH15_GATK directory, look at the contents and read the extremely brief README.txt file.

Refresh your memory of the topic and scientific context of the workshop: 10-20 minutes

  • Open the PDF document called ASHG2015Tutorial-Appendix.
  • Read the introduction. If any of the content is especially new or confusing to you, consider following the links included to the additional documentation on our website. We will cover this content briefly at the start of the tutorial, but the more you prepare, the better your workshop experience will be.

Install and test software: 30-45 minutes

Go over the second part of the ASHG2015Tutorial-Appendix document to acquaint yourself with the technical requirements of the workshop and follow the detailed installation instructions. In particular:

  • Make sure you have the correct version of Java installed (Java 7 / JRE 1.7).
  • Download all 3 software packages (GATK, Samtools, IGV) to the laptop you will bring to the workshop.
  • Copy the program files of all three to the ASGH15_GATK` directory.
  • Run the test commands for GATK and Samtools, and launch IGV.

If you are new to the command line or GATK, we strongly recommend reviewing the sections of the document about tool syntax (pages 8-10) and practicing basic Unix commands. You may also benefit from spending some time gaining familiarity with IGV.


We're hiring! It must be Monday. Aug 17

Much like the universe and my belt size, the GATK methods development team aims to grow ever larger.

The job titles on the docket this week are Data Scientist and Computational Biologist; the job description is below or on LinkedIn.


New patch version 3.4-46 released Jul 9

This patch release fixes several issues that we felt were annoying enough to warrant an interim version release; see detailed list below.

Oh, and in case you're curious about the patch number, the *-46 numeral refers to the number of code commits made since the 3.4-0 release. Out of this, about a dozen are related to the bug fixes listed above; another dozen relate to new work that is not yet publicly available (gotta wait 'til 3.5...) and the rest are automated commits produced when merging completed work into the master codebase.


Broad Institute and Google Genomics launch GATK as a Service Jun 24

It’s an exciting week here at GATK HQ because we finally get to tell you about this very cool project we’ve been working on: today, Broad and Google announced plans to make GATK available as a service on Google Cloud Platform as part of Google Genomics!

Our goal with this project is to enable researchers around the world to run the latest version of the GATK Best Practices pipeline without the hassle of figuring out the plumbing or storing huge amounts of genomic data locally. The initial alpha rollout will be limited to a small set of users. Based on our experience supporting the GATK user community, we think this will dramatically lower the barriers to top-notch genomic analysis capabilities, especially for researchers who don’t have access to the kind of dedicated compute infrastructure and engineering teams required for analyzing genomic data at scale.

Rest assured, if you’re the do-it-yourselfer type, the DIY GATK option is still here; you’ll still be able to download the latest version of GATK from the Broad website, set it up on your own system and run it locally. We will continue documenting and supporting this option with the same level of dedication as ever.

You can read more about the details in the Broad Institute press release and on the Google Cloud Platform blog. Feel free to ask questions in the comments thread of course. We’ll keep you posted here as we move forward.

Workshop presentations -- 2015 Pretoria, South Africa 6/22-26 Jun 22

The slides from the workshop presentations as well as related materials will be posted here at the end of each day:

Website down for server maintenance over the weekend Jun 13

The GATK website will be down at some point over the weekend between Saturday and Sunday night due to maintenance operations on the Broad servers. We don't know exactly what will be the time and the duration of the outage -- hopefully it will be brief.

The forum itself (including the documentation articles) will remain available, although the styling and layout may be affected.

Apologies for the late notice.

Have a great weekend and we'll see you on the other side.

Update to the accelerated PairHMM library for IBM POWER8 systems Jun 2

The Ubuntu version of the library provided by IBM to accelerate HaplotypeCaller on their POWER8 systems (originally described here) has been updated to fix a bug. You can download it from the original DropBox link.

Holiday notice -- forum on hiatus, service resumes May 26 May 23

As the USA will be observing Memorial Day on Monday 25, forum support will be (mostly) unavailable until Tuesday 26.

I say mostly because some of us have been known to sneak away from friends and family to secretly answer forum questions on their smartphone. Which is terrible social etiquette and must be strictly discouraged, of course.

To anyone in the USA and abroad who will be enjoying a long weekend, have a great time, and do spare a thought for the men and women whose service and sacrifices we honor on this occasion.

To the rest of y'all, sorry folks! But I'm sure you have holidays we don't have :)

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GATK Dev Team


RT @WileyGenetics: #ASHG15 Tomorrow morning's #GATK has sold out! But don't fret! You can still learn how to use #GATK here:…
8 Oct 15
RT @dgmacarthur: AH: we'll shortly be rolling out an ExAC update that flags phase-dependent variants; GATK now automatically outputs phase …
8 Oct 15
#GATK poster is online at for anyone who missed it at #ASHG15
8 Oct 15
Bring on the 20,000 WGS! Great test of the #GATK's GVCF workflow at the next order of scale since ExAC
8 Oct 15
@WileyGenetics No worries, thx for trying to boost the paper's visibility. But our software made an evolutionary jump in the meantime.
8 Oct 15