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
- Puhti: 0.0.0.2016_01_04.cc14e52
Usage
To use XHMM, load the module:
module load xhmm
After that XHMM starts with command:
xhmm