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General description

AlphaFamImpute is a genotype calling, phasing, and imputation algorithm for large full-sib families in diploid plants and animals which supports individuals genotyped with SNP array or GBS data. The approach draws heavily on single and multi-locus iterative peeling (as in AlphaPeel). It also has been inspired by work outside our group such as hs-phase (Ferdosi et al. 2014), and magicimpute (Zheng et al. 2018). AlphaFamImpute was written by Andrew Whalen, and is currently being supported by Andrew Whalen and Steve Thorn.

Please email any questions to alphagenes@roslin.ed.ac.uk.


Commercial use

AlphaFamImpute is part of a suite of software that our group has developed. It is fully and freely available for academic use, provided that users cite it in publications. However, due to our contractual obligations with some of the funders of the research program that has developed this suite of software, all interested commercial organisations are requested to contact John Hickey (john.hickey@roslin.ed.ac.uk) to discuss the terms of use.


Citation

Coming soon.


Downloads

Version 0.0.1 (December 2019)

The AlphaFamImpute download contains a python wheel file, a manual, and two example datasets. Please report any bugs or errors to alphagenes@roslin.ed.ac.uk.

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