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

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GATK Dev Team


@BrianPardy Great, thanks for the feedback!
28 Sep 16
@BrianPardy Thank you! Does anything in particular stand out? We'd love to know what people find most useful so we can do more of the same.
28 Sep 16
#GATK workshop crew is in Basel, ready to roll! @ISBSIB
25 Sep 16
@thatdnaguy That's right, we've retired it, see
23 Sep 16
@geoffjentry @BroadGenomics Ah, you should ask @WDL_dev on the WDL forum then :)
21 Sep 16

Our favorite tweets from others

I've easily written my first custom ReadFilter for GATK. The @gatk_dev 's toolkit is a great example of programming.
21 Sep 16
@gatk_dev "make it so"
8 Sep 16
it's the nightly build owl for GATK :D
11 Aug 16
We're going to make an hg38 version of ExAC. And we'll make @dgmacarthur pay for it. #BioinformaticsCampaignPromises
2 Aug 16
You’re right @gatk_dev honesty is key! About variants manual filtering: “In any case you're probably in for a world of pain.” Ha now I know!
11 Jul 16
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