If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Genome STRiP Functions
The building blocks for Genome STRiP are built out of GATK Walkers and some
miscellaneous command line utilities.
If you need to implement a specialized pipeline, you can use these modules
directly, using the standard Queue pipelines as a guide. The standard Queue
pipelines also use Samtools, BWA and some Picard utilities.
2. GATK Walkers
This section documents various utilities and walkers that are not yet available in the production release. These utilities may be available in some of the interim releases (build snapshots) downloadable from our website http://www.broadinstitute.org/software/genomestrip.