I see CallSegments mentioned in a few tutorials and posts. However, there does not seem to be any documentation for it. Is it possible to get more info? Is that basically the next version of ReCapSeg?
Sort of, yes. It's part of a suite of tools for calling CNVs that is available as part of the GATK4 alpha package. Although the CNV tools themselves are ready to be used, the GATK4 package is still in development, and we don't yet have a good way to provide online docs -- but we're working on it. In the meantime you would have to invoke the CLI help function. There is a software+data bundle you can download from the Downloads page, see Workshop Bundles.
Thanks for clarifying! Do you have any benchmarks or comparisons for the GATK4 CNV tools? Were they introduced to make GATK more comprehensive or are there clear advantages to current methods?