AlphaAssign is a parentage assignment algorithm. This program uses a likelihood based model to determine the sire of an individual based on a list of potential sires. AlphaAssign differs from other parentage assignment algorithms by having the option to use phase information to determine parentage. For more information on the algorithm see Parentage assignment with genotyping‐by‐sequencing data, Journal of Animal Breeding and Genetics.
AlphaAssign is part of a suite of software that our group has developed for imputation. It is fully and freely available to all academics. User are however requested to credit its use on any publications. However, due to our contractual obligations with some of funders of the research program that has developed this suite of software all commercial organisations that wish to use it are requested to contact John Hickey (email@example.com) to discuss the terms under which it can be used.
1. User Manual
Click here to see the pdf version.
2. Python files for Linux, Mac and Windows
The AlphaAssign folders contains Python 3.6 scripts for AlphaAssign, along with an example folder which contains a sample spec file and pipeline for performing hybrid peeling with sequence data. AlphaAssign requires the module plinkio to run (available via pip).