rbpisupati / rabbit

A Mathematica pipeline for genetic analysis in multiparental populations

RABBIT

RABBIT was developped for Reconstrucing Ancestral Blocks BIT by bit in multiparental populations, which has been extended for genotype imputaiton and genetic map construction. Tested in Matheamtica 11.0. Adapted for Mathematica 12.0 in RABBITv3.2.

##Getting started

1. Clone or download.

2. Create a new mathematica notebook in a work folder, and set path to the folder "RABBIT_Packages".

3. Needs["MagicReconstruct`"] for haplotype reconstruciton.

   Needs["MagicImpute`"] for genotype imputation

   Needs["MagicMap`"] and myParallelNeeds["MagicMap`"] for genetic map construction

4. Manual in the folder "RABBIT_Manual", examples in the folder "RABBIT_Example Scripts", and tutorials in the folder "RABBIT_Tutorial"

##References

Zheng, C., Boer, M. P., and Eeuwijk, F. A. 2014. A general modeling framework for genome ancestral origins in multi-parental populations. Genetics. 198: 87-101.

Zheng, C. 2015. Modeling X-linked ancestral origins in multiparental populations. G3: Genes | Genomes | Genetics. 5: 777-801.

Zheng, C., Boer, M. P., and Eeuwijk, F. A. 2015. Reconstruction of genome ancestry blocks in multiparental populations. Genetics. 200: 1073-1087.

Zheng, C., Boer, M. P., and Eeuwijk, F. A. 2018. Recursive algorithms for modeling genome blocks in a fixed pedigree. G3: Genes | Genomes | Genetics. 8: 3231–3245

Zheng, C., Boer, M. P., and Eeuwijk, F. A. 2018. Accurate genotype imputation in multiparental populations from low-coverage sequence. Genetics. 210: 71-82.

Zheng, C., Boer, M. P., and Eeuwijk, F. A. 2019. Construction of genetic linkage maps in multiparental populations. Submitted.