RABBIT

A statistical pipeline for genetic analysis in connected multiparental (diploid) populations

Features

• Functions include data filtering, map construction, genotype imputation, and haplotype reconstruction.
• Apply to many multiparental populations with shared inbred or outbred parents
• Account for various sequencing errors such as allelic bias
• Efficient for genomic data with hundreds of thousands of markers

License

The software is licensed under PolyForm Strict License 1.0.0. For commercial use, a (paid) license agreement needs to be set up. To obtain the license agreement, contact rabbit-support@wur.nl.

Document

See RABBITManual for the detailed online document.

Install

1. Download and install Julia available at https://julialang.org/
2. Download RABBIT repository
3. In a command shell, run

path/to/bin/julia.exe path/to/install_RABBIT.jl

Alternatively, from the Julia (>=v1.9.7, 64-bit) REPL, run

julia>include("path/to/install_RABBIT.jl")

Similarly, use uninstall_RABBIT.jl to uninstall RABBIT, and use test_RABBIT.jl to test RABBIT.

Packages

RABBIT consists of a set of Julia packages. Here is a list of key packages.

Package name	Description
MagicBase	Basic data structures and functions
MagicSimulate	Simulation of genotypic/phenotypic data
MagicFilter	Filter genotypic data
MagicCall	Single marker genotype calling
MagicMap	Linkage map construction
MagicImpute	Genotype imputation
MagicReconstruct	Haplotype reconstruction
MagicScan	QTL scan (EXPERIMENT)

Run RABBIT in Julia REPL

Load package

To load a package for data analysis such as genotype imputatioin, run

using MagicImpute

Run function

Generally, RABBIT requires two inputs: genofile and pedinfo. The following is an overview of key functions.

magicsimulate("founderhaplo.vcf.gz","ped.csv")
magicfilter("geno.vcf.gz","ped.csv")
magiccall("geno.vcf.gz","ped.csv")
magicmap("geno.vcf.gz","ped.csv")
magicimpute("geno.vcf.gz","ped.csv"; mapfile="outstem_magicmap_construct_map.csv.gz")
magicreconstruct("geno.vcf.gz","ped.csv")

Help

To get help for a function such as magicimpute, run

?magicimpute

Run RABBIT in a command line.

The RABBIT CLI is a collection of main function files that are located in the download RABBIT repository folder RABBITCLI; each file is a wrapper of the corresponding julia function.

Run main function file

Change into work directory including input files, and run a main function file in a command shell,

path/to/bin/julia.exe path/to/RABBITCLI/src/rabbit_function.jl -g geno.vcf.gz -p ped.csv

We will assume that the paths to julia.exe and the main function file have been added in the platform environmental variable PATH.

julia rabbit_function.jl -g geno.vcf.gz -p ped.csv

The following is an overview of the key main function files:

julia rabbit_magicfilter.jl -g geno.vcf.gz -p ped.csv
julia rabbit_magiccall.jl -g geno.vcf.gz -p ped.csv
julia rabbit_magicmap.jl -g geno.vcf.gz -p ped.csv
julia rabbit_magicimpute.jl -g geno.vcf.gz -p ped.csv --mapfile outstem_magicmap_construct_map.csv.gz
julia rabbit_magicreconstruct.jl -g geno.vcf.gz -p ped.csv

Help

To get help for each main function file, run

julia rabbit_function.jl -h