README.md

In mtmcgowan/GGcall: Clusters Infinium SNP chip data in polyploid species and calls genotypes

GGcall: Gaussian Genotype Calling

An R package for calling polyploid SNP chip data using Gaussian mixture models.

Author: Matthew McGowan

Overview

GGcall is an R pipeline for clustering complex signals generated by the Illumina Infinium assays when used in polyploid species. The only input requirement is an R/Theta export generated from a Genome Studio Project. After clustering, users have the option to interactively filter, plot, and call genotypes. Final calls are output in a simple numerical format for further imputation and use in genome-wide-associaton-studies or genomic-selection analysis.

Requirements

R/Rstudio (version 3.4 or higher)

A spreadsheet editor (Excel, OpenOffice-Calc, Numbers, etc.)

Installation

The easiest way to get GGcall is to install the package using devtools. If you don't have devtools already installed: ```{r, eval = FALSE} install.packages("devtools")

Load devtools and then install GGcall from Github:
```{r, eval = FALSE}
library(devtools)
devtools::install_github("mtmcgowan/GGcall")

Usage

The easiest way to learn to use GGcall is to go through the tutorial provided here: Guided Tutorial

Depending on your population size and marker number, it may be useful to use a high-performance cluster to speed up the clustering step.

Getting help

The best way to get help is to submit an issue on Github. Before submitting, be sure to clearly describe the problem and provide a reproducible example.

More Information

An earlier version of GGcall was presented at the 2018 Plant and Animal Genome Conference. Here is a poster that provides more information for how it works:

mtmcgowan/GGcall documentation built on July 1, 2021, 4:14 a.m.