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.
The AlphaFamImpute.zip file contains a python3 wheel file, a manual, and an example dataset.
AlphaFamImpute 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.
Andrew Whalen, Gregor Gorjanc, John M Hickey, AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data, Bioinformatics, Volume 36, Issue 15, 1 August 2020, Pages 4369–4371, https://doi.org/10.1093/bioinformatics/btaa499