# HMM copy number variation calling
[](https://travis-ci.org/kylessmith/hmmCNV) [](https://badge.fury.io/py/hmmCNV)
[](https://www.buymeacoffee.com/kylessmith)
This is a Python package for Copy Number Variation
detection using an HMM as implemented in [ichorCNA][code].
All citations should reference to [original paper][paper].
## Install
If you dont already have numpy and scipy installed, it is best to download
`Anaconda`, a python distribution that has them included.
```
https://continuum.io/downloads
```
Dependencies can be installed by:
```
pip install -r requirements.txt
```
PyPI install, presuming you have all its requirements installed:
```
pip install hmmCNV
```
## Usage
```python
from hmmCNV import hmmCNV
# Call CNVs for bin data
loglik, hmm_results = hmmCNV.hmmCNV(tumour_copy, verbose=True)
```
[code]: https://github.com/broadinstitute/ichorCNA
[paper]: https://www.nature.com/articles/s41467-017-00965-y
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