1 Abstract
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 log10(p-values), enabling identification and plotting of QTL. The source code is available at https://github.com/bmansfeld/QTLseqr.
Core ideas
An R package that performs Next Generation Sequencing Bulk Segregant Analysis was developed
Two methods for analysis are provided: QTL-seq and G’
The QTLseqr package is quick and produces publication quality figures and tables
Footnotes
- Abbreviation list
- BSA
- bulk segregant analysis
- FDR
- false discovery rate
- LD
- linkage disequilibrium
- NGS
- next generation sequencing
- QTL
- quantitative trait locus
- SNP
- single nucleotide polymorphism