RABBIT

A statistical pipeline for genetic analysis in connected multiparental 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 balance bias
• Efficient for genomic data with hundreds of thousands of markers

Installation

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/RABBIT/install_RABBIT.jl

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

include("path/to/RABBIT/install_RABBIT.jl")

Similarly, use uninstall_RABBIT.jl for uninstalling RABBIT, up_RABBIT.jl for updating RABBIT, version_RABBIT.jl for printing the version number of each package in RABBIT, and test_RABBIT.jl for testing RABBIT (running the full test might take around one hour).

Packages

Here is a list of key packages in RABBIT: MagicBase provides functions for visualizing or summarizing results, and each of MagicSimulate, MagicFilter, MagicCall, MagicMap, MagicImpute, MagicReconstruct, and MagicScan performs a single data analysis with function name being the lowercase of the package name.

HMM, Pedigrees, MagicPrior, MagicLD, MagicLinkage and SpectralEmbedding are supporting packages. RABBITCLI includes RABBIT's Command Line Interface (CLI). RABBITDocs is only for automatically generating documents. All packages are installed in order by running install_RABBIT.jl as described above.

Versions

The RABBITCLI version is the same as that of RABBIT. To check the versions of the RABBIT packages, run

using RABBITCLI
rabbitversion()