It is recommended you use at least 40 samples with this method.
One should also have more _covered_ target regions than there are samples.
This means this method is not suited for very small target kits.
Please note that it is _not_ possible to run this method without GATK dependencies.
Additional optional config values:
| Namespace | Name | Type | Default | Meaning |
| --------- | ---- | ---- | ------- | ------- |
| xhmm_normalize | normalize_method | String | PVE_mean | The normalization method to use |
| xhmm_normalize | pve_mean_factor | Float | 0.7 | Factor for PVE mean normalization |
**XHMM example**
```yaml
kopisu:
use_cnmops_method:false
use_freec_method:false
use_xhmm_method:true
amplicon_bed:<path_to_bed>
xhmm:
discover_params:<path_to_file>
exe:<path_to_executable>
```
## Getting Help
If you have any questions on running Kopisu, suggestions on how to improve the overall flow, or requests for your favorite CNV related program to be added, feel free to post an issue to our issue tracker at [GitHub](https://github.com/biopet/biopet).
Or contact us directly via: [SASC email](mailto:SASC@lumc.nl)