https://github.com/biona001/fastphase.jl

Julia wrapper for the fastPHASE genetics software (this is WIP)
https://github.com/biona001/fastphase.jl

Last synced: 4 days ago
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Julia wrapper for the fastPHASE genetics software (this is WIP)

• Host: GitHub
• URL: https://github.com/biona001/fastphase.jl
• Owner: biona001
• License: other
• Created: 2022-01-22T02:19:11.000Z (almost 3 years ago)
• Default Branch: master
• Last Pushed: 2024-04-13T02:12:21.000Z (7 months ago)
• Last Synced: 2024-04-14T00:58:03.808Z (7 months ago)
• Language: Julia
• Homepage:
• Size: 756 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# fastPHASE.jl

| **Documentation** | **Build Status** | **Code Coverage**  |

|-------------------|------------------|--------------------|

| [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://biona001.github.io/fastPHASE.jl/dev/) [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://biona001.github.io/fastPHASE.jl/stable/) | [![build Actions Status](https://github.com/biona001/fastPHASE.jl/workflows/CI/badge.svg)](https://github.com/biona001/fastPHASE.jl/actions) | [![codecov](https://codecov.io/gh/biona001/fastPHASE.jl/branch/master/graph/badge.svg?token=YyPqiFpIM1)](https://codecov.io/gh/biona001/fastPHASE.jl) |

fastPHASE.jl is a Julia wrapper of the popular [fastPHASE](https://stephenslab.uchicago.edu/software.html#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](https://doi.org/10.1086/502802)

## Supported data files

The original input format for fastPHASE is outdated. See their original [documentation](http://scheet.org/code/fastphase_doc_1.4.pdf).

fastPHASE.jl supports binary PLINK inputs via [SnpArrays.jl](https://github.com/OpenMendel/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

```julia

using Pkg

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

```

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