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 firstname.lastname@example.org.
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 email@example.com.