Service Notice: Due to the blizzard currently hammering the US Northeast, the Broad is shut down and the GATK forum will be mostly unattended while we hunker down and sip hot cocoa with marshmallows. Assuming the power stays on and we're able to dig ourselves out of the snow when it's all over, normal service should resume Wednesday or Thursday.
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