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:


rpoplin


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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I added a video to a @YouTube playlist https://t.co/XbziUTyDMy 2017-07-23 Kate Voss "Full stack genomics pipelining with GATK4 + WDL +
6 Aug 17
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@CuiJack No sorry, GGA mode is not yet supported in GATK4 HaplotypeCaller.
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Amazing session @edgenome with @gatk_dev comes to an end. Enriched learning! Thx #gatk #gatk2017 #Genomics #Edinburgh #Bioinformatics
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18 Jul 17
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