DOI: 10.18129/B9.bioc.DOQTL    

Genotyping and QTL Mapping in DO Mice

Bioconductor version: Release (3.6)

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.

Author: Daniel Gatti, Karl Broman, Andrey Shabalin, Petr Simecek

Maintainer: Daniel Gatti <Dan.Gatti at>

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biocViews GeneticVariability, Genetics, HiddenMarkovModel, SNP, Software
Version 1.14.0
In Bioconductor since BioC 3.0 (R-3.1) (3.5 years)
License GPL-3
Depends R (>= 3.0.0), BSgenome.Mmusculus.UCSC.mm10, GenomicRanges, VariantAnnotation
Imports annotate, annotationTools, biomaRt, Biobase, BiocGenerics, corpcor, doParallel, foreach, fpc, hwriter, IRanges, iterators, mclust, QTLRel, regress, rhdf5, Rsamtools, RUnit, XML
Suggests MUGAExampleData, doMPI
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