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The XHMM (eXome-Hidden Markov Model) C++ software suite calls copy number variation (CNV) from next-generation sequencing projects, where exome capture was used (or targeted sequencing, more generally). Specifically, XHMM uses principal component analysis (PCA) normalization and a hidden Markov model (HMM) to detect and genotype copy number variation (CNV) from normalized read-depth data from targeted sequencing experiments. Please see the XHMM website for more information.
Documentation for XHMM