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AlphaPeel

AlphaPeel is a software package for calling, phasing, and imputing genotype and sequence data in pedigree populations. This program implements single-locus peeling, multi-locus peeling, and hybrid peeling. A complete description of these methods is given in the suggested citation:

Whalen, A, Ros-Freixedes, R, Wilson, DL, Gorjanc, G, Hickey, JM. (2018). Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees. Genetics Selection Evolution; doi: https://doi.org/10.1186/s12711-018-0438-2

User guide

See https://alphapeel.readthedocs.io/en/latest

Conditions of use

AlphaPeel is fully and freely available for all use under the MIT License.

Requirements

  • Python 3
  • NumPy
  • Numba

Installation

AlphaPeel is available on PyPI:

pip install AlphaPeel

Distribution

Wheel distribution and source distribution are both available on PyPI.

Build wheels

If you want to build the wheels yourself, we require an installation of Python 3 and you need to fork and clone the repository to your local directory first (see user guide)

Run the following to build the wheel distribution and the source distribution of the package.

First, create the virtual environment:

python3 -m venv AlphaPeel_env

Next, activate the environment:

source AlphaPeel_env/bin/activate

Install build:

python3 -m pip install --upgrade build

Build the distribution:

python3 -m build

Now, the distributions of AlphaPeel should be available in dist/.

Finally, deactivate the environment:

deactivate