fastPHASE.jl

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fastPHASE.jl is a Julia wrapper of the popular fastPHASE genetics program, designed for haplotype reconstruction and estimating missing genotypes from population data.

The methodology is described in the following paper

• Scheet, P and Stephens, M (2006). A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. https://doi.org/10.1086/502802

Supported data files

The original input format for fastPHASE is outdated. See their original documentation.

fastPHASE.jl supports binary PLINK inputs via SnpArrays.jl, by simply decompressing and converting binary PLINK data into the format that is readable by fastPHASE. Thus, it is not advised to run this on large (e.g. > 1GB PLINK) data.

Adding VCF, BGEN, and PGEN support in this manner via corresponding OpenMendel modules should not be hard. PRs are welcomed!

Installation

fastPHASE.jl requires Julia v1.6 or later. It is not yet registered and can be installed by

using Pkg
pkg"add https://github.com/biona001/fastPHASE.jl"

The original fastPHASE software thus fastPHASE.jl only support Linux and MacOS.