DOI: 10.18129/B9.bioc.GBScleanR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see GBScleanR.

Error correction tool for noisy genotyping by sequencing (GBS) data

Bioconductor version: 3.17

GBScleanR is a package for quality check, filtering, and error correction of genotype data derived from next generation sequcener (NGS) based genotyping platforms. GBScleanR takes Variant Call Format (VCF) file as input. The main function of this package is `estGeno()` which estimates the true genotypes of samples from given read counts for genotype markers using a hidden Markov model with incorporating uneven observation ratio of allelic reads. This implementation gives robust genotype estimation even in noisy genotype data usually observed in Genotyping-By-Sequnencing (GBS) and similar methods, e.g. RADseq. The current implementation accepts genotype data of a diploid population at any generation of multi-parental cross, e.g. biparental F2 from inbred parents, biparental F2 from outbred parents, and 8-way recombinant inbred lines (8-way RILs) which can be refered to as MAGIC population.

Author: Tomoyuki Furuta [aut, cre]

Maintainer: Tomoyuki Furuta <f.tomoyuki at>

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biocViews GeneticVariability, Genetics, HiddenMarkovModel, QualityControl, SNP, Sequencing, Software
Version 1.4.4
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License GPL-3 + file LICENSE
Depends SeqArray
Imports stats, utils, methods, ggplot2, tidyr, expm, Rcpp, RcppParallel, gdsfmt
LinkingTo Rcpp, RcppParallel
Suggests BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown
SystemRequirements GNU make, C++11
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