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# GBScelaneR ![GBScleanR_icon]( Error correction tool for genotype data derived from reduced representation sequencing(RRS). ## Introduction `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 allele 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. ## Installation You can install `GBScleanR` from the Bioconductor repository with running the following code on an R console. Currently `GBScleanR` is listed in the developmental package repository of Bioconductor( You need to set to use Bioc devel as shown below. On the other hand, `GBScleanR` on the GitHub repository provide you the latest package with some developmental functions. If you need the stable release version of the package, please install the one on Bioconductor. From Bioconductor: ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("GBScleanR") ``` From GitHub: ``` if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") devtools::install_github("tomoyukif/GBScleanR", build_vignettes = TRUE) ``` For more information see vignette or run the following code on a R console. ``` browseVignettes(package = "GBScleanR") ``` ## Citations In preparation for publication...