This is the Linux app named cnvCapSeq whose latest release can be downloaded as cnvCapSeq-0.1.2.zip. It can be run online in the free hosting provider OnWorks for workstations.
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cvnCapSeq is a set of Java-based command-line tools for detecting and genotyping copy number variation (CNV) in targeted resequencing experiments of large contiguous genomic regions.
This is an application that can also be fetched from https://sourceforge.net/projects/cnvcapseq/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.