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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.


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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.


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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:

https://drive.google.com/folderview?id=0BwTg3aXzGxEDVk5RcEF3WW1SQWM&usp=sharing


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 :)


Version highlights for GATK version 3.4 May 22

Folks, I’m all out of banter for this one, so let’s go straight to the facts. GATK 3.4 contains a shedload of improvements and bug fixes, including some new functionality that we hope you’ll find useful. The full list is available in the detailed release notes.

None of the recent changes involves any disruption to the Best Practice workflow (I hear some sighs of relief) but you’ll definitely want to check out the tweaks we made to the joint discovery tools (HaplotypeCaller, CombineGVCFs and GenotypeGVCFs), which are rapidly maturing as they log more flight time at Broad and in the wild.


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Release notes for GATK version 3.4 May 15

GATK 3.4 was released on May 15, 2015. Itemized changes are listed below. For more details, see the user-friendly version highlights to be published soon.

Note that the release is in progress at time of posting -- it may take a couple of hours before the new GATK jar file is updated on the downloads page.


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Workshop presentations -- 2015 UK 4/20-24 Apr 19

The presentation slides from the 2015 "GATK in the UK" workshop (April 20-24) are available on DropBox here.

All slides will ultimately be posted in the Presentations section of the Guide.



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GATK Dev Team

@gatk_dev

@samstudio8 Fun and interesting blog post! Our docs team will clarify the filter doc; code holds ultimate answer https://t.co/pN50hHQ71Z
4 Sep 15
@gatoravi Thx :) Credit goes to wider DSDE team (of which we are a subset) https://t.co/fclufciDI4
4 Sep 15
@rtyags yes, totally fine with citation. If u can, let us know which fig(s) so we know what ppl find esp useful.
4 Sep 15
RT @erlichya: LOL! "Lior's blog is known for its specificity but less for its sensitivity" - @GenomeNathan intro to @lpachter seminar at @n…
27 Aug 15
RT @thatdnaguy: **VERY IMP. #GATK BUG WARNING** Do not run GenotypeGVCFs on gzipped and tabix indexed files. Increased runtime ** ~70X ** …
27 Aug 15