Open AccessQTLseqr: An R Package for Bulk Segregant Analysis with Next‐Generation Sequencing
Author(s) -
Mansfeld Ben N.,
Grumet Rebecca
Publication year - 2018
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2018.01.0006
Subject(s) - quantitative trait locus , r package , biology , statistic , identification (biology) , computational biology , snp , genetics , computer science , single nucleotide polymorphism , statistics , mathematics , genotype , gene , botany
Next-Generation Sequencing Bulk Segregant Analysis (NGS-BSA) is efficient in detecting quantitative trait loci (QTL). Despite the popularity of NGS-BSA and the R statistical platform, no R packages are currently available for NGS-BSA. We present QTLseqr, an R package for NGS-BSA that identifies QTL using two statistical approaches: QTL-seq and G'. These approaches use a simulation method and a tricube smoothed G statistic, respectively, to identify and assess statistical significance of QTL. QTLseqr can import and filter SNP data, calculate SNP distributions, relative allele frequencies, G' values, and log (-values), enabling identification and plotting of QTL. The source code is available at .