Harald Ringbauer, Yilei Huang, May 2022; Code released under GNU General Public License v3.0
This is the code repository intended for contributing developers (i.e. to manage code used in development and publications). The release for users is made available as an installable Python software package hapROH. The official user documentation is available at readthedocs. It contains quick-start guides as well as usage examples on test data.
There are three main parts of the hapROH package:
Software to call ROH from ancient and present-day DNA using reference haplotypes. Author: Harald Ringbauer, September 2020 Code released under GNU General Public License v3.0
Development Code behind python package hapROH. Please refer to our online documentation for details about the current version and installation.
This is the git repository for development, as well as code used in the hapROH publication.
hapCon is an extension of hapROH for estimaing contamination rate for male aDNA samples.
We have prepared a detailed online documentation for hapCon. In addition, a jupyter notebook guide for using our method is availble at ./Notebooks/Vignettes/hapCon_vignette.ipynb in this repository. We also have a preprint for hapCon if you are interested in more technical details and its usage limits.
Joint estimation of ROH blocks and Contamination Rate
Please refer to our readthedocs site for details.
You only need to install the PyPi package hapROH to use both hapCon and hapROH:
To install via pip:
pip install hapROH
To upgrade an existing installation:
pip install --upgrade hapROH
Scientific manuscripts introducing the methods are available at:
- https://doi.org/10.1038/s41467-021-25289-w for hapROH
- https://doi.org/10.1101/2021.12.20.473429 for hapCon