GenotypeR: An integrated r package for single nucleotide polymorphism genotype marker design and data analysis

Abstract

Abstract Single nucleotide polymorphism (SNP) genotyping is an important tool to understand basic and applied questions, such as genomic structure, recombination, introgression, parentage/pedigrees and the genetic basis of traits, among other things. Each of these applications share a similar workflow: marker design, genotyping and data analysis. In this manuscript, we present genotypeR, a package that implements a common genotyping workflow with a standardized software interface. The genotypeR package is written in r with integration of a marker design pipeline written in Perl. genotypeR designs SNP genotyping markers from vcf files produced from variant calling of sequence data. These markers are processed before genotyping to ensure that they can be used in downstream analyses. After marker multiplexing suitability has been conducted on the genotyping platform, genotyping is conducted and raw output from the genotyping assay is processed by genotypeR. The primary post‐genotyping functionality includes commonly used QA/QC procedures, genotype conversions, recombination analysis and data export to a popular program that uses genotyping data (rqtl). genotypeR provides a unified software environment for analysing SNP genotyping data, and will be useful for researchers investigating various research questions, removing the need for individual researchers to write custom software, and facilitating a common workflow.