The XHMM C++ software suite was written to call copy number variation (CNV) from next-generation sequencing projects, where exome capture was used (or targeted sequencing, more generally).
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Using XHMM Software to Detect Copy Number Variation in Whole-Exome Sequencing Data.
Fromer M, Purcell SM.
Curr Protoc Hum Genet. 2014 Apr 24;81:7.23.1-7.23.21. doi: 10.1002/0471142905.hg0723s81.