DOQTL: Genotyping and QTL Mapping in DO Mice

DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.

Package details

AuthorDaniel Gatti, Karl Broman, Andrey Shabalin, Petr Simecek
Bioconductor views GeneticVariability Genetics HiddenMarkovModel SNP
MaintainerDaniel Gatti <>
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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DOQTL documentation built on May 6, 2019, 3:09 a.m.