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). It works for us and for our collaborators, however, since we aim to publish it, we would like to get some feedback before - is the readme readable? is the installation and file preparation easy? what can be improved?
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.
PS Yes, I can pack it as R package, but I do not see a huge advantage of this.
PPS I got couple of questions at my mailbox, however, I think it make sense to post anything of general interest here, so I encourage you to add comments / answers with questions or advices or criticism here and please please please let me know if nothing works.
UPD the preprint is here, somatic part of ClinCNV. Please, criticize it. Not sure if I am gonna to submit it somewhere, but at least I would like to update it, taking into account your critics. https://www.biorxiv.org/content/10.1101/837971v1