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

- Recent posts

- Upcoming events

See Events calendar for full list and dates

- Recent events

See Events calendar for full list and dates

- Follow us on Twitter

GATK Dev Team


Still a 1-in-3 chance of winning one of the 100 prizes we're giving to survey respondents! Tell your friends and la…
17 Nov 17
@ctsa11 @strnr Fair enough; now that we have 280 characters to play with we can say != "GVCF as we define it" (with…
17 Nov 17
#GATK HaplotypeCaller paper on biorxiv #BetterLateThanNever
17 Nov 17
Thanks again for inviting us to @marshallu, we had a great time and enjoyed the very active group of participants!
13 Nov 17
@geoffjentry It's so nice to be able to use proper grammar and spelling... #GrammarPolice
9 Nov 17

- Our favorite tweets from others

Wanna be a baller, HaplotypeCaller 20K genotypes in the VCF file Caller, gettin' phased tonight
17 Nov 17
This amazing genomics toolkit helps researchers find insights that save lives - I know! GATK users - please provide…
2 Nov 17
using GATK to identify SNPs while handing out candy... Happy Halloween! @broadinstitute @gatk_dev #bioinformatics #researchisfun #Halloween
31 Oct 17
Although it made me cry sometimes, I owe them a lot and love them much more.
16 Oct 17
Round of applause at #BOSC2017 for GATK4 being open sourced.
23 Jul 17
See more of our favorite tweets...