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XHMM (eXome-Hidden Markov Model)


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).

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.

XHMM was explicitly designed to be used with targeted exome sequencing at high coverage (at least 60x - 100x) using Illumina HiSeq (or similar) sequencing of at least ~50 samples. However, no part of XHMM explicitly requires these particular experimental conditions, just high coverage of genomic regions for many samples.


Software is free to use and open source, but no license specified.


  • xhmm 1.0 is available in Puhti


To use XHMM, load the biokit module:

module load biokit

After that XHMM starts with command:


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Last edited Mon Mar 29 2021