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.
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.