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


I added a video to a @YouTube playlist 2017-07-23 Kate Voss "Full stack genomics pipelining with GATK4 + WDL +
6 Aug 17
RT @IntelHealth: Learn about the Genomics Kernel Library (GKL), which helps developers accelerate #genomics applications.
3 Aug 17
RT @dgmacarthur: Work with my team to help change the lives of rare disease patients. Software engineering and compbio roles open: https://…
1 Aug 17
@CuiJack No sorry, GGA mode is not yet supported in GATK4 HaplotypeCaller.
1 Aug 17
I added a video to a @YouTube playlist Broad Institute — GATK in the Cloud: Running genomics pipelines at
29 Jul 17

- Our favorite tweets from others

Round of applause at #BOSC2017 for GATK4 being open sourced.
23 Jul 17
Round of applause for @Katewanders - Broad Institute will open source data science tools from now on #BOSC2017
23 Jul 17
The @gatk_dev team, that delivered an excellent "GATK Best Practices for Variant Discovery" workshop this week, on…
20 Jul 17
Amazing session @edgenome with @gatk_dev comes to an end. Enriched learning! Thx #gatk #gatk2017 #Genomics #Edinburgh #Bioinformatics
19 Jul 17
Great day of lectures on GATK Best Practices yesterday. Very clear and useful. Thanks! @gatk_dev @edgenome
18 Jul 17
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