AlphaPeel 1.1.3

Multilocus and hybrid peeling

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 Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees, Genetics Selection Evolution.

User guide

See docs/source/index.rst or PDF in the ZIP file in this repository.

Conditions of use

AlphaPeel is part of a suite of software that our group has developed. It is fully and freely available for all use under the MIT License.

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

Requirements

• Python 3
• NumPy
• Numba

Installation

wget https://github.com/AlphaGenes/AlphaPeel/raw/main/AlphaPeel.zip
unzip AlphaPeel.zip
pip install AlphaPeel/AlphaPeel*.whl

Build instructions

Run the following to build the Python wheel and user guide. You will need an installation of Sphinx and LaTex to build the user guide.

git clone --recurse-submodules https://github.com/AlphaGenes/AlphaPeel.git
cd AlphaPeel

mamba create -n AlphaPeel
mamba activate AlphaPeel
mamba install python=3.9
pip install sphinx
./build_pipeline.sh
pip install --force-reinstall dist/AlphaPeel*.whl

cd example; ./runScript.sh

The wheel can be found in dist/ and PDF of the user guide at docs/build/latex/alphaplantimpute2.pdf