Dear community members,
we've prepared a tool for CNV detection (another one) called ClinCNV. It was already used for the analysis of around 5 thousands of samples sequenced on different platforms and the results are quite good, we also performed the benchmarking and found out that the tool is at least not worse than the competitors in germline context and works better for somatic context (using False Discovery Rate and concordance as metrics). You can check out a short presentation of the tool here (around 60 slides).
The tool uses cohorts of samples and read-depth (and BAF for somatic calling). It has quite a lot of features, such as clustering of samples prior to analysis, IGV visualization, polymorphic regions calling, mosaic CNV calling, different options for FDR control, etc. To have a quick overview I'd recommend to go directly to the docs. Try the test run with the command from here.
The limiting factor may be - we used ngs-bits for files preparation, however, it is an easy-to-install package, it is fast and has many useful features.
Please send me any feedback about the tool.
UPD the preprint is here, somatic part of ClinCNV. Please, criticize it. https://www.biorxiv.org/content/10.1101/837971v1