created by Geraldine_VdAuwera
on 2013-07-09
Before the workshop, you should run through this tutorial to install all the software on your laptop:
- [Install necessary software](http://www.broadinstitute.org/gatk/guide/article?id=2899)
We use a small test dataset that you can download from this link (1.1 Gb):
- https://s3.amazonaws.com/gatk-workshop/mini-bundle.zip
During the hands-on session of the workshop, we walk through the following tutorials, with some minor modifications:
- [Revert a BAM](http://www.broadinstitute.org/gatk/guide/article?id=2908)
- [Prepare the reference](http://www.broadinstitute.org/gatk/guide/article?id=2798)
- [Map and mark duplicates](http://www.broadinstitute.org/gatk/guide/article?id=2799)
- [Local alignment around indels](http://www.broadinstitute.org/gatk/guide/article?id=2800)
- [Base Recalibration](http://www.broadinstitute.org/gatk/guide/article?id=2801)
- [Compression with ReduceReads](http://www.broadinstitute.org/gatk/guide/article?id=2802)
- [Call variants with HaplotypeCaller](http://www.broadinstitute.org/gatk/guide/article?id=2803)
- [Call variants with UnifiedGenotyper](http://www.broadinstitute.org/gatk/guide/article?id=2804)
tutorials, official, workshop
Updated on 2013-07-17
From rpoplin on 2013-07-09
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!