GATK version 4.beta.2
(i.e. the second beta release) is out. See the GATK4 BETA
page for download and details.
ReCapSeg is a tool for performing analysis of somatic Copy Number Variation. Note that this version of the tools (implemented in Python) is being replaced by a new version (implemented in Java) that is now available in the GATK 4 alpha preview. See http://gatkforums.broadinstitute.org/categories/gatk-4-alpha for documentation on the new CNV workflow.