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XHMM (eXome-Hidden Markov Model)

Description

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.

License

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

Version

  • xhmm 1.0 is available in Puhti

Usage

To use XHMM, load the biokit module:

module load biokit

After that XHMM starts with command:

xhmm

More information

Last edited Mon Mar 29 2021