Before the workshop, you should run through this tutorial to install all the software on your laptop:

We use a small test dataset that you can download from this link (1.1 Gb):

During the hands-on session of the workshop, we walk through the following tutorials, with some minor modifications:


Hi workshopers, I was asked to post a link to the prebuilt GATK and Queue jars for people who are on the Broad file system. They are automatically linked to the most recent release. /humgen/gsa-hpprojects/GATK/bin/current /humgen/gsa-hpprojects/Queue/bin/current Cheers!

Tue 9 Jul 2013

At a glance

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GATK Dev Team


@nialljlennon Wait, Banks is spinning off his own unofficial #GATK workshop series now? Usurper! :D
28 Feb 17
@ninadoak There's a variety of options available, you'll have to be a bit more specific on what you're trying to do...
28 Feb 17
This short video series provides 5-min overviews of the key parts of the #GATK Best Practices workflows.
28 Feb 17
@watsonhaigh It's not currently possible. If you explain the use case on the forum we can consider a feature request.
27 Feb 17
@vibbioinfocore Thanks for having us over! Great group of participants, lots of good questions!
25 Feb 17

Our favorite tweets from others

From the @gatk_dev page describing .vcf files: "Don't write home-brewed VCF parsing scripts. It never ends well”
28 Feb 17
Our 3-day course on GATK finished - 38 participants very happy! Big thanks to @gatk_dev team for excellent lessons.
24 Feb 17
@froggleston @dgmacarthur Sounds like ExAC is reaching Uber stage. ‘Uber but for pizza’. ‘ExAC but for wheat’.
14 Jan 17
#ESRenpeinture grad school - postdoc - after postdoc
6 Jan 17
Really happy to have you again this year! @VIBLifeSciences
3 Jan 17
See more of our favorite tweets...
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