HaploTool’s documentation

Contents:

Overview

HaploTool helps to visualize genomic region of interest (e.g. candidate gene region) and associate haplotype goups with phenotype. It can be used to validate markers by visually and analytically confirming association of a marker with a haplotype that is associated with desirable trait.

See Quick start page for an example of basic usage.

Features

  • Import data in various formats (HapMap, PLINK)
  • Marker and sample QC and filtering ( see Quality control and filtering )
  • Haplotype clustering into groups and visualization
  • Visualization of phenotype along with genotype ordered according to haplotype groups
  • Testing association between markers and haplotypes

Install

You can use HaploTool running as an online service on GOBii Marker Portal (link), or you can install it on your local machine either as R package or using Docker.

The details are described on the Bitbucket page:

http://gobiin1.bti.cornell.edu:6083/projects/UT/repos/haplotool/browse/README.md

Briefly, there are two options, we recommend using Docker.

  1. Installing using RStudio
  1. Download R package archive (link)
  2. In RStudio:
  • Go to menu Tools -> Install Packages
  • In the “Install from..” dropdown, select “Package Archive File” and click “Install”
  1. Instal and run using Docker:
docker run -dti \
--name=shiny_app \
-h shiny-node \
-v /home/gadm/workspace/haplotool:/home/shiny/haplotool \
--user shiny \
--rm \
-p 80:3838 \
gadm01/haplotool:v0.1

Support

If you are having issues, please let us know at d [dot] chebotarov [at] irri.org

Any feedback (bugs, feature requests) is welcome.

License

HaploTool will be licensed under an open-source license suitable for GOBii Project once it is published. Please check back for updates.

Credits

HaploTool was developed by Dmytro Chebotarov for the GOBii Project under direction of Elizabeth Jones and with extensive discussions with:

  • Joshua N. Cobb
  • Partha S. Biswas
  • Juan David Arbelaez Velez
  • Ramil Mauleon
  • Nickolai Alexandrov

We thank Roy Lawrence Petrie for testing Docker and handling the deployment of the tool.

We thank Ken L. McNally and the bioinformatics team at International Rice Research Institute as well as early users at IRRI and other CGIAR centers for testing out the tool and all their input.