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.

• XHMM (eXome-Hidden Markov Model)
  • License
  • Available
  • Usage
  • More information

License

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

Available

• Puhti: 0.0.0.2016_01_04.cc14e52

Usage

To use XHMM, load the module:

module load xhmm

After that, XHMM starts with the command:

xhmm

More information

• XHMM home page

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