An imputation software for massive livestock populations.
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AlphaImpute2
AlphaImpute2 is a phasing and imputation algorithm for massive livestock populations. The method uses a approximate version of multi-locus iterative peeling for pedigree based imputation, and a novel imputation algorithm that uses the Positional Burrows Wheeler Transform for population imputation. AlphaImpute2 has been successfully used to perform imputation in populations of hundreds of thousands of individuals. AlphaImpute2 was developed by Andrew Whalen, and is currently being supported by Andrew Whalen and Steve Thorn.
User guide
See https://alphapeel.readthedocs.io/en/latest
Installation
AlphaImpute2 is available on PyPI:
pip install AlphaImpute2
Example
An example dataset and corresponding script are available in the example/ folder.
Conditions of use
AlphaImpute2 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, J.M. Hickey, (2020), AlphaImpute2: Fast and accurate pedigree and population based imputation for hundreds of thousands of individuals in livestock populations, bioRxiv.https://doi.org/10.1101/2020.09.16.299677
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